>AFI247 (AFI247Q) /CSM/AF/AFI2-B/AFI247Q.Seq.d/
AATGATGAAAAAAAATAAACCAACAGTAGCACAAACTTTATCACCAGAAGAAGAACAAGC
AAAATTCTTTGAAGAAGCTAAAAACAATGTTATGATTCAAGGTCATCACATGAAATTATC
TTTGGATAACTCAAAATTAATGGATGCACTCAAGTATGCCTCAAACATTATCAATGAACT
CCGTACAAGTTTACTTTCACCAAAATCATATTATGCTCTCTATTTAGTTGCTTTTGATTA
TCTTCAATACTTGAATACTTATCTCTATGAAGAGAAACATGGTAAGAAAATGATTGAACT
TTATGAAGTTGTACAACATGCTGGTAATGTTTTACCAAGATTATATTTATTAATTACAGT
TGGATCAGTTTATATTAAAACTAAACAAGCACCAGCAAAAGATGTATTAAAAGATTTAAT
TGAAATGTGTAGAGGTGTTCAACATCCAACAAGAGGTTTATTTTTAAGACATTATCTTAG
TGAAGTTACCAAAGATAAATTACCAGATATTGATTCATCCGTTGAGAATGGTACAGTTAT
GGATTCAATTGATTTCATCATTCAAAATTTCACAGAGACXXXXXXXXXXGAAAATAAATG
GATTGCAATTGGTTCAAAGATTTTCACCTTTGTCAGTGAAACCATCAAAGCTTTGGCCGA
TATCAAATTGGCCGATCTTAGCTTTAGATTATACCTTCAAGCACTCCAAACCTTTGACCA
CTGTGGTTTGGTCTCTCGTGTCAAAGAATTGGCCATCAAGGCTCTCTTAATCTTCCAAGA
AGATATCGCCGATTTCAAAGCTCAAGTTATGGCCCTTCAATTGTTAATCTCTACTCTCAA
TAGTTTAAGCATTCCAAATGAAGAGATCTATGAATCCTTGGCCGCCCAAACCATTAAACA
AGCTTCTCGTCTTCTCTTACCACAAGATCAAGCAAAACTCATCTCTACTTGTTCACATTT
ATTCTGGGTTGATAATCCTTCTCGTCAATATCAAAATCCAGACTCTGTATTACAAGCTCT
CAAAAAAGCTCTCTCCATTATCAGTAATGAATCGAGTCCTGGTCTTGGTACATTTGTTGA
CATTTTGAATGAATGTCTCTTCTATTGTGATAAAGAAACTGATGCTGTTCCAATTCAATT
CGTTTCAGATTTGGTTGAATTAATTCGTACTACTCATGTTAAAGAAGCTGATCCAGCATT
ACCATATTTACAAAATACTATCNAATACATTCAAT

MMKKNKPTVAQTLSPEEEQAKFFEEAKNNVMIQGHHMKLSLDNSKLMDALKYASNIINEL
RTSLLSPKSYYALYLVAFDYLQYLNTYLYEEKHGKKMIELYEVVQHAGNVLPRLYLLITV
GSVYIKTKQAPAKDVLKDLIEMCRGVQHPTRGLFLRHYLSEVTKDKLPDIDSSVENGTVM
DSIDFIIQNFTE---

---ENKWIAIGSKIFTFVSETIKALADIKLADLSFRLYLQALQTFDHCGLVSRVKELAIK
ALLIFQEDIADFKAQVMALQLLISTLNSLSIPNEEIYESLAAQTIKQASRLLLPQDQAKL
ISTCSHLFWVDNPSRQYQNPDSVLQALKKALSIISNESSPGLGTFVDILNECLFYCDKET
DAVPIQFVSDLVELIRTTHVKEADPALPYLQNTIXYIQ

Frame A:
ndekk*tnsstnfitrrrtskil*rs*kqcydsrssheiifg*lkingctqvclkhyq*t
pykftftkiilcslfscf*lssileylsl*retw*end*tl*scttcw*cftkiifinys
wisly*n*tstskrcikrfn*nv*rcstsnkrfifktls**syqr*itry*fir*ewysy
gfn*fhhskfhrd---

---ENKWIAIGSKIFTFVSETIKALADIKLADLSFRLYLQALQTFDHCGLVSRVKELAIK
ALLIFQEDIADFKAQVMALQLLISTLNSLSIPNEEIYESLAAQTIKQASRLLLPQDQAKL
ISTCSHLFWVDNPSRQYQNPDSVLQALKKALSIISNESSPGLGTFVDILNECLFYCDKET
DAVPIQFVSDLVELIRTTHVKEADPALPYLQNTIXYIQ

Frame B:
MMKKNKPTVAQTLSPEEEQAKFFEEAKNNVMIQGHHMKLSLDNSKLMDALKYASNIINEL
RTSLLSPKSYYALYLVAFDYLQYLNTYLYEEKHGKKMIELYEVVQHAGNVLPRLYLLITV
GSVYIKTKQAPAKDVLKDLIEMCRGVQHPTRGLFLRHYLSEVTKDKLPDIDSSVENGTVM
DSIDFIIQNFTE---

---kinglqlvqrfsplsvkpsklwpisnwpilaldytfkhskplttvvwslvsknwpsr
ls*sskkispisklklwpfnc*sllsiv*afqmkrsmnpwppkplnkllvfsyhkikqns
sllvhiysgliillvnikiqtlyyklskklsplsvmnrvlvlvhlltf*mnvssivikkl
mlfqfnsfqiwln*fvllmlkkliqhyhiykilsntfn

Frame C:
**kkinqq*hklyhqkknkqnslkklktml*fkvit*nylwitqn*wmhssmpqtlsmns
vqvyfhqnhimlsi*llliifnt*ilismkrnmvrk*lnfmklynmlvmfyqdyiy*lql
dqfilklnkhqqkmy*ki*lkcvevfniqqevyf*diilvklpkinyqilihplrmvqlw
iqlissfkisqr---

---k*mdcnwfkdfhlcq*nhqsfgryqigrs*l*iipsstpnl*plwfglscqrighqg
slnlprryrrfqsssygpsivnlysq*fkhsk*rdl*ilgrpnh*tsfssslttrsskth
lylftfilg**sfssisksrlcitssqksslhyq**ieswswyic*hfe*mslll**rn*
ccsnsirfrfg*insyysc*rs*ssitiftkyyxihs

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

AFI247 (AFI247Q) /CSM/AF/AFI2-B/AFI247Q.Seq.d/                       2353   0.0
VHK662 (VHK662Q) /CSM/VH/VHK6-C/VHK662Q.Seq.d/                       1275   0.0
VHJ813 (VHJ813Q) /CSM/VH/VHJ8-A/VHJ813Q.Seq.d/                       1275   0.0
VHI583 (VHI583Q) /CSM/VH/VHI5-D/VHI583Q.Seq.d/                       1275   0.0
VHH532 (VHH532Q) /CSM/VH/VHH5-B/VHH532Q.Seq.d/                       1275   0.0
CFF491 (CFF491Q) /CSM/CF/CFF4-D/CFF491Q.Seq.d/                       1275   0.0
AHH565 (AHH565Q) /CSM/AH/AHH5-C/AHH565Q.Seq.d/                       1275   0.0
AHA519 (AHA519Q) /CSM/AH/AHA5-A/AHA519Q.Seq.d/                       1275   0.0
AHO859 (AHO859Q) /CSM/AH/AHO8-C/AHO859Q.Seq.d/                       1269   0.0
VHI863 (VHI863Q) /CSM/VH/VHI8-C/VHI863Q.Seq.d/                       1267   0.0

                                                             Score    E
Sequences producing significant alignments:                  (bits) Value  N

BE844390|BE844390.1 EST134 Apis mellifera female antennae Lambda ZAP II library Apisproteins of mammals, mRNA sequence.    56   5e-10  2
AZ685086|AZ685086.1 ENTMW65TR Entamoeba histolytica Sheared DNA Entamoeba histolytica genomic, DNA sequence.    64   3e-09  3
AY193838|AY193838.1 Entamoeba histolytica vacuolar sorting protein 35-like (Vps35) gene, partial cds.    64   8e-09  3
AZ533812|AZ533812.1 ENTDW59TR Entamoeba histolytica Sheared DNA Entamoeba histolytica genomic, DNA sequence.    58   2e-07  3
AZ691304|AZ691304.1 ENTLW09TR Entamoeba histolytica Sheared DNA Entamoeba histolytica genomic, DNA sequence.    64   5e-06  1
AP003132|AP003132.2 Staphylococcus aureus subsp. aureus N315 genomic DNA, complete genome, section 4/10.    38   7e-04  12
AP004825|AP004825.1 Staphylococcus aureus subsp. aureus MW2 DNA, complete genome, strain:MW2, section 4/10.    38   0.001  11
BP188068|BP188068.1 Dugesia japonica cDNA, clone: 01668_HH, expressed in the head.    48   0.002  3
AP003361|AP003361.3 Staphylococcus aureus subsp. aureus Mu50 DNA, complete genome, section 4/9.    38   0.015  11
AE017339|AE017339.1 Mycoplasma mobile 163K section 3 of 3 of the complete genome.    36   0.043  10

                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

(Q54C24) RecName: Full=Vacuolar sorting protein 35;                   416   e-115
AM425621_1(AM425621|pid:none) Vitis vinifera contig VV78X235801....   207   4e-52
T08858(T08858)vacuolar protein-sorting protein homolog A_TM017A0...   198   3e-49
E84556(E84556)probable vacuolar sorting-associated protein [impo...   198   3e-49
BT008553_1(BT008553|pid:none) Arabidopsis thaliana clone U50265 ...   198   3e-49
AC149634_2(AC149634|pid:none) Medicago truncatula clone mth2-5i1...   194   7e-48
AL928906_3(AL928906|pid:none) Zebrafish DNA sequence from clone ...   191   3e-47
BC117573_1(BC117573|pid:none) Danio rerio zgc:136268, mRNA (cDNA...   191   3e-47
BT059024_1(BT059024|pid:none) Salmo salar clone ssal-rgf-521-005...   191   4e-47
AK223218_1(AK223218|pid:none) Homo sapiens mRNA for vacuolar pro...   190   7e-47

 psg: 0.81  gvh: 0.23  alm: 0.38  top: 0.53  tms: 0.00  mit: 0.31  mip: 0.00
 nuc: 0.00  erl: 0.00  erm: 0.00  pox: 0.00  px2: 0.50  vac: 0.00  rnp: 0.00
 act: 0.00  caa: 0.00  yqr: 0.00  tyr: 0.00  leu: 0.00  gpi: 0.00  myr: 0.00
 dna: 0.00  rib: 0.00  bac: 0.00  m1a: 0.00  m1b: 0.00  m2 : 0.00  mNt: 0.00
 m3a: 0.00  m3b: 0.00  m_ : 1.00 

	 56.0 %: nuclear
	 36.0 %: cytoplasmic
	  4.0 %: mitochondrial
	  4.0 %: endoplasmic reticulum

>> prediction for AFI247 is nuc

>AFI247F.Seq
AATGATGAAAAAAAATAAACCAACAGTAGCACAAACTTTATCACCAGAAGAAGAACAAGC
AAAATTCTTTGAAGAAGCTAAAAACAATGTTATGATTCAAGGTCATCACATGAAATTATC
TTTGGATAACTCAAAATTAATGGATGCACTCAAGTATGCCTCAAACATTATCAATGAACT
CCGTACAAGTTTACTTTCACCAAAATCATATTATGCTCTCTATTTAGTTGCTTTTGATTA
TCTTCAATACTTGAATACTTATCTCTATGAAGAGAAACATGGTAAGAAAATGATTGAACT
TTATGAAGTTGTACAACATGCTGGTAATGTTTTACCAAGATTATATTTATTAATTACAGT
TGGATCAGTTTATATTAAAACTAAACAAGCACCAGCAAAAGATGTATTAAAAGATTTAAT
TGAAATGTGTAGAGGTGTTCAACATCCAACAAGAGGTTTATTTTTAAGACATTATCTTAG
TGAAGTTACCAAAGATAAATTACCAGATATTGATTCATCCGTTGAGAATGGTACAGTTAT
GGATTCAATTGATTTCATCATTCAAAATTTCACAGAGAC----------

>AFI247Z.Seq
----------GAAAATAAATGGATTGCAATTGGTTCAAAGATTTTCACCTTTGTCAGTGA
AACCATCAAAGCTTTGGCCGATATCAAATTGGCCGATCTTAGCTTTAGATTATACCTTCA
AGCACTCCAAACCTTTGACCACTGTGGTTTGGTCTCTCGTGTCAAAGAATTGGCCATCAA
GGCTCTCTTAATCTTCCAAGAAGATATCGCCGATTTCAAAGCTCAAGTTATGGCCCTTCA
ATTGTTAATCTCTACTCTCAATAGTTTAAGCATTCCAAATGAAGAGATCTATGAATCCTT
GGCCGCCCAAACCATTAAACAAGCTTCTCGTCTTCTCTTACCACAAGATCAAGCAAAACT
CATCTCTACTTGTTCACATTTATTCTGGGTTGATAATCCTTCTCGTCAATATCAAAATCC
AGACTCTGTATTACAAGCTCTCAAAAAAGCTCTCTCCATTATCAGTAATGAATCGAGTCC
TGGTCTTGGTACATTTGTTGACATTTTGAATGAATGTCTCTTCTATTGTGATAAAGAAAC
TGATGCTGTTCCAATTCAATTCGTTTCAGATTTGGTTGAATTAATTCGTACTACTCATGT
TAAAGAAGCTGATCCAGCATTACCATATTTACAAAATACTATCNAATACATTCAAT

>AFI247P.Seq
AATGATGAAAAAAAATAAACCAACAGTAGCACAAACTTTATCACCAGAAGAAGAACAAGC
AAAATTCTTTGAAGAAGCTAAAAACAATGTTATGATTCAAGGTCATCACATGAAATTATC
TTTGGATAACTCAAAATTAATGGATGCACTCAAGTATGCCTCAAACATTATCAATGAACT
CCGTACAAGTTTACTTTCACCAAAATCATATTATGCTCTCTATTTAGTTGCTTTTGATTA
TCTTCAATACTTGAATACTTATCTCTATGAAGAGAAACATGGTAAGAAAATGATTGAACT
TTATGAAGTTGTACAACATGCTGGTAATGTTTTACCAAGATTATATTTATTAATTACAGT
TGGATCAGTTTATATTAAAACTAAACAAGCACCAGCAAAAGATGTATTAAAAGATTTAAT
TGAAATGTGTAGAGGTGTTCAACATCCAACAAGAGGTTTATTTTTAAGACATTATCTTAG
TGAAGTTACCAAAGATAAATTACCAGATATTGATTCATCCGTTGAGAATGGTACAGTTAT
GGATTCAATTGATTTCATCATTCAAAATTTCACAGAGAC----------GAAAATAAATG
GATTGCAATTGGTTCAAAGATTTTCACCTTTGTCAGTGAAACCATCAAAGCTTTGGCCGA
TATCAAATTGGCCGATCTTAGCTTTAGATTATACCTTCAAGCACTCCAAACCTTTGACCA
CTGTGGTTTGGTCTCTCGTGTCAAAGAATTGGCCATCAAGGCTCTCTTAATCTTCCAAGA
AGATATCGCCGATTTCAAAGCTCAAGTTATGGCCCTTCAATTGTTAATCTCTACTCTCAA
TAGTTTAAGCATTCCAAATGAAGAGATCTATGAATCCTTGGCCGCCCAAACCATTAAACA
AGCTTCTCGTCTTCTCTTACCACAAGATCAAGCAAAACTCATCTCTACTTGTTCACATTT
ATTCTGGGTTGATAATCCTTCTCGTCAATATCAAAATCCAGACTCTGTATTACAAGCTCT
CAAAAAAGCTCTCTCCATTATCAGTAATGAATCGAGTCCTGGTCTTGGTACATTTGTTGA
CATTTTGAATGAATGTCTCTTCTATTGTGATAAAGAAACTGATGCTGTTCCAATTCAATT
CGTTTCAGATTTGGTTGAATTAATTCGTACTACTCATGTTAAAGAAGCTGATCCAGCATT
ACCATATTTACAAAATACTATCNAATACATTCAAT