RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6709
(288 letters)
>gnl|CDD|233003 TIGR00512, salvage_mtnA, S-methyl-5-thioribose-1-phosphate
isomerase. The delineation of this family was based in
part on a discussion and neighbor-joining phylogenetic
study, by Kyrpides and Woese, of archaeal and other
proteins homologous to the alpha, beta, and delta
subunits of eukaryotic initiation factor 2B (eIF-2B), a
five-subunit molecule that catalyzes GTP recycling for
eIF-2. This clade is now recognized to include the
methionine salvage pathway enzyme MtnA [Amino acid
biosynthesis, Aspartate family].
Length = 331
Score = 170 bits (434), Expect = 3e-51
Identities = 73/168 (43%), Positives = 95/168 (56%), Gaps = 22/168 (13%)
Query: 122 ATAEYGTALGVIRSLHGANKIVDIKDKQFPDNDSLEKYVGEKLDYLVSARPTAVNMKRAA 181
A YG AL ++ + + + + EKL YLVS+RPTAVN+ A
Sbjct: 50 IVAAYGLALAA---------------READEREEFKALLEEKLQYLVSSRPTAVNLSWAL 94
Query: 182 DSVKSSLSEWAKASPVNTVKTRLIQLIESMLEKDISDNKAIGRNGAQALIDLNPGVS-KL 240
D ++++L A V +K L+ E +LE+D+ DN+AIG NGA + GV+ L
Sbjct: 95 DRMRAALE---AAKTVADIKEALLAEAERILEEDLEDNRAIGENGAALIK---KGVAAPL 148
Query: 241 NVLTHCNTGSLATAEYGTALGVIRSLHGANKIGAAYCTETRPYNQGAR 288
VLTHCNTGSLATA YGTALGVIRS H ++ Y ETRP QGAR
Sbjct: 149 RVLTHCNTGSLATAGYGTALGVIRSAHEKGRLEHVYADETRPRLQGAR 196
Score = 160 bits (407), Expect = 3e-47
Identities = 73/214 (34%), Positives = 98/214 (45%), Gaps = 59/214 (27%)
Query: 5 QSIIYEKHSLKILDQLLLPHTSKLVDINNVEDAYQAIKSMQVRGAPAIAIVGCLGLVVDI 64
++I + + SL++LDQ LLPH S+ +++ VED AI+ M+VRGAPAI IV GL +
Sbjct: 1 RAIKWNRGSLELLDQRLLPHESEYIEVTTVEDVADAIRDMRVRGAPAIGIVAAYGLALAA 60
Query: 65 KDKQFPDN--------------------------------------------ELIQLIES 80
++ + L+ E
Sbjct: 61 READEREEFKALLEEKLQYLVSSRPTAVNLSWALDRMRAALEAAKTVADIKEALLAEAER 120
Query: 81 MLEKDISDNKAIGRNGAQALIDLNPRVSKLNVLTHCNTGSLATAEYGTALGVIRSLHGAN 140
+LE+D+ DN+AIG NGA + L VLTHCNTGSLATA YGTALGVIRS H
Sbjct: 121 ILEEDLEDNRAIGENGAALIKKGVAA--PLRVLTHCNTGSLATAGYGTALGVIRSAHEKG 178
Query: 141 KIVDIKDKQFPDNDSLEKYVGEKLDYLVSARPTA 174
++ + Y E L AR TA
Sbjct: 179 RLEHV-------------YADETRPRLQGARLTA 199
>gnl|CDD|223260 COG0182, COG0182, Predicted translation initiation factor 2B
subunit, eIF-2B alpha/beta/delta family [Translation,
ribosomal structure and biogenesis].
Length = 346
Score = 142 bits (361), Expect = 3e-40
Identities = 65/167 (38%), Positives = 83/167 (49%), Gaps = 21/167 (12%)
Query: 122 ATAEYGTALGVIRSLHGANKIVDIKDKQFPDNDSLEKYVGEKLDYLVSARPTAVNMKRAA 181
A YG AL S K + + + + + L S RPTAVN+ A
Sbjct: 54 VAAAYGLALAARES------------KNDSKGEEFIEALEKAAETLKSTRPTAVNLFWAL 101
Query: 182 DSVKSSLSEWAKASPVNTVKTRLIQLIESMLEKDISDNKAIGRNGAQALIDLNPGVSKLN 241
D + ++ E A V K ++Q E + E+D+ N+AIG NGA+ L D
Sbjct: 102 DRMLNAAKE---AIEVKEPKESILQEAEEIAEEDLEANRAIGENGAELLPD------GDT 152
Query: 242 VLTHCNTGSLATAEYGTALGVIRSLHGANKIGAAYCTETRPYNQGAR 288
VLTHCN G+LAT YGTALGVIRS H K + ETRPY QGAR
Sbjct: 153 VLTHCNAGALATVGYGTALGVIRSAHEEGKDIRVFADETRPYLQGAR 199
Score = 136 bits (344), Expect = 6e-38
Identities = 70/221 (31%), Positives = 93/221 (42%), Gaps = 67/221 (30%)
Query: 2 KSLQSIIY-EKHSLKILDQLLLPHTSKLVDINNVEDAYQAIKSMQVRGAPAIAIVGCLGL 60
L+ I + + S+K+LDQ LLP K V+ ED +AIK M VRGAPAI + GL
Sbjct: 1 MKLRPIEWKDDGSVKLLDQRLLPFEEKYVECKTYEDVAEAIKDMVVRGAPAIGVAAAYGL 60
Query: 61 VV-----------------------------------------------DIKDKQFPDNE 73
+ + + + P
Sbjct: 61 ALAARESKNDSKGEEFIEALEKAAETLKSTRPTAVNLFWALDRMLNAAKEAIEVKEPKES 120
Query: 74 LIQLIESMLEKDISDNKAIGRNGAQALIDLNPRVSKLNVLTHCNTGSLATAEYGTALGVI 133
++Q E + E+D+ N+AIG NGA+ L D VLTHCN G+LAT YGTALGVI
Sbjct: 121 ILQEAEEIAEEDLEANRAIGENGAELLPD------GDTVLTHCNAGALATVGYGTALGVI 174
Query: 134 RSLHGANKIVDIKDKQFPDNDSLEKYVGEKLDYLVSARPTA 174
RS H K + + + E YL AR TA
Sbjct: 175 RSAHEEGKDIRV-------------FADETRPYLQGARLTA 202
>gnl|CDD|233008 TIGR00524, eIF-2B_rel, eIF-2B alpha/beta/delta-related
uncharacterized proteins. This model, eIF-2B_rel,
describes half of a superfamily, where the other half
consists of eukaryotic translation initiation factor 2B
(eIF-2B) subunits alpha, beta, and delta. It is unclear
whether the eIF-2B_rel set is monophyletic, or whether
they are all more closely related to each other than to
any eIF-2B subunit because the eIF-2B clade is highly
derived. Members of this branch of the family are all
uncharacterized with respect to function and are found
in the Archaea, Bacteria, and Eukarya, although a number
are described as putative translation intiation factor
components. Proteins found by eIF-2B_rel include at
least three clades, including a set of uncharacterized
eukaryotic proteins, a set found in some but not all
Archaea, and a set universal so far among the Archaea
and closely related to several uncharacterized bacterial
proteins [Unknown function, General].
Length = 303
Score = 121 bits (305), Expect = 1e-32
Identities = 58/167 (34%), Positives = 84/167 (50%), Gaps = 22/167 (13%)
Query: 122 ATAEYGTALGVIRSLHGANKIVDIKDKQFPDNDSLEKYVGEKLDYLVSARPTAVNMKRAA 181
A YG AL + + + + ++ + + D+L+S RPTAVN+ A
Sbjct: 24 VAAAYGLALAA-------------RKIETDNVEEFKEDLEKAADFLLSTRPTAVNLFWAL 70
Query: 182 DSVKSSLSEWAKASPVNTVKTRLIQLIESMLEKDISDNKAIGRNGAQALIDLNPGVSKLN 241
+ V +S V K L++ ++E+D+ N+ IG NGA+ + D
Sbjct: 71 ERVLNSAE---NGESVEEAKESLLREAIEIIEEDLETNRKIGENGAKLIKD------GDT 121
Query: 242 VLTHCNTGSLATAEYGTALGVIRSLHGANKIGAAYCTETRPYNQGAR 288
VLTHCN G+LAT++YGTALGVIRS K ETRP NQG+R
Sbjct: 122 VLTHCNAGALATSDYGTALGVIRSAWEDGKRIRVIACETRPRNQGSR 168
Score = 89.4 bits (222), Expect = 9e-21
Identities = 48/161 (29%), Positives = 67/161 (41%), Gaps = 52/161 (32%)
Query: 31 INNVEDAYQAIKSMQVRGAPAIAIVGCLGLVVDIKDKQFPDNE----------------- 73
ED AIKSM VRGAPAI + GL + + + + E
Sbjct: 1 CRTYEDVADAIKSMVVRGAPAIGVAAAYGLALAARKIETDNVEEFKEDLEKAADFLLSTR 60
Query: 74 -----------------------------LIQLIESMLEKDISDNKAIGRNGAQALIDLN 104
L++ ++E+D+ N+ IG NGA+ + D
Sbjct: 61 PTAVNLFWALERVLNSAENGESVEEAKESLLREAIEIIEEDLETNRKIGENGAKLIKD-- 118
Query: 105 PRVSKLNVLTHCNTGSLATAEYGTALGVIRSLHGANKIVDI 145
VLTHCN G+LAT++YGTALGVIRS K + +
Sbjct: 119 ----GDTVLTHCNAGALATSDYGTALGVIRSAWEDGKRIRV 155
>gnl|CDD|235578 PRK05720, mtnA, methylthioribose-1-phosphate isomerase; Reviewed.
Length = 344
Score = 121 bits (305), Expect = 3e-32
Identities = 55/169 (32%), Positives = 72/169 (42%), Gaps = 27/169 (15%)
Query: 122 ATAEYGTALGV--IRSLHGANKIVDIKDKQFPDNDSLEKYVGEKLDYLVSARPTAVNMKR 179
A YG AL S G + K + E YL ++RPTAVN+
Sbjct: 53 IAAAYGMALAAREDASDDGEEFL---------------KKLEEAAAYLAASRPTAVNLFW 97
Query: 180 AADSVKSSLSEWAKASPVNTVKTRLIQLIESMLEKDISDNKAIGRNGAQALIDLNPGVSK 239
A D ++ L+ P K L + + E+D+ N+AIG +G +
Sbjct: 98 ALDRMREVLAP----LPGAERKAALEEEAIEIHEEDVEINRAIGEHGLTLIRK------G 147
Query: 240 LNVLTHCNTGSLATAEYGTALGVIRSLHGANKIGAAYCTETRPYNQGAR 288
+LTHCN G LATA YGTAL I + Y ETRP QGAR
Sbjct: 148 QGILTHCNAGWLATAGYGTALAPIYAAKEKGIDIHVYADETRPRLQGAR 196
Score = 111 bits (279), Expect = 2e-28
Identities = 53/214 (24%), Positives = 79/214 (36%), Gaps = 64/214 (29%)
Query: 6 SIIYEKHSLKILDQLLLPHTSKLVDINNVEDAYQAIKSMQVRGAPAIAIVGCLGLVV--- 62
+ ++ +++ILDQ LPH + V++ E+ AI+ M VRGAPAI I G+ +
Sbjct: 5 PVAWKDGAVRILDQRKLPHEVEYVELTTAEEVADAIRDMVVRGAPAIGIAAAYGMALAAR 64
Query: 63 DIKDKQFPDNE-------------------LIQLIESML--------------------- 82
+ + L ++ M
Sbjct: 65 EDASDDGEEFLKKLEEAAAYLAASRPTAVNLFWALDRMREVLAPLPGAERKAALEEEAIE 124
Query: 83 --EKDISDNKAIGRNGAQALIDLNPRVSKLNVLTHCNTGSLATAEYGTALGVIRSLHGAN 140
E+D+ N+AIG +G + +LTHCN G LATA YGTAL I +
Sbjct: 125 IHEEDVEINRAIGEHGLTLIRK------GQGILTHCNAGWLATAGYGTALAPIYAAKEKG 178
Query: 141 KIVDIKDKQFPDNDSLEKYVGEKLDYLVSARPTA 174
+ + Y E L AR TA
Sbjct: 179 IDIHV-------------YADETRPRLQGARLTA 199
>gnl|CDD|180362 PRK06036, PRK06036, translation initiation factor IF-2B subunit
alpha; Provisional.
Length = 339
Score = 99.0 bits (247), Expect = 5e-24
Identities = 60/167 (35%), Positives = 81/167 (48%), Gaps = 22/167 (13%)
Query: 122 ATAEYGTALGVIRSLHGANKIVDIKDKQFPDNDSLEKYVGEKLDYLVSARPTAVNMKRAA 181
A YG AL S + D D L K + + L S RPTAVN+
Sbjct: 53 AAGGYGIALAARLS-------------KAKDVDELLKDLKVAAETLKSTRPTAVNLSWGV 99
Query: 182 DSVKSSLSEWAKASPVNTVKTRLIQLIESMLEKDISDNKAIGRNGAQALIDLNPGVSKLN 241
D V + + A V ++ ++ E + E+D++ NK IG++GA+ L D +
Sbjct: 100 DRVLKAALD---AEDVEEIRDIALREAERIAEEDVARNKLIGKHGAKLLEDGD------T 150
Query: 242 VLTHCNTGSLATAEYGTALGVIRSLHGANKIGAAYCTETRPYNQGAR 288
VLTHCN G LA ++GTALGVIRS K ETRP NQG+R
Sbjct: 151 VLTHCNAGRLACVDWGTALGVIRSAVEQGKEIKVIACETRPLNQGSR 197
Score = 89.4 bits (222), Expect = 1e-20
Identities = 52/172 (30%), Positives = 81/172 (47%), Gaps = 52/172 (30%)
Query: 10 EKHSLKILDQLLLPHTSKLVDINNVEDAYQAIKSMQVRGAPAIAIVGCLGLVVDIKDKQF 69
E +S+K++DQ LLP K+++ +E +AIKS++VRGAPA+ G G+ + + +
Sbjct: 9 ESNSVKLIDQTLLPEEYKVIECKTLESLCEAIKSLRVRGAPALGAAGGYGIALAARLSKA 68
Query: 70 PDNE----------------------------------------------LIQLIESMLE 83
D + ++ E + E
Sbjct: 69 KDVDELLKDLKVAAETLKSTRPTAVNLSWGVDRVLKAALDAEDVEEIRDIALREAERIAE 128
Query: 84 KDISDNKAIGRNGAQALIDLNPRVSKLNVLTHCNTGSLATAEYGTALGVIRS 135
+D++ NK IG++GA+ L D + VLTHCN G LA ++GTALGVIRS
Sbjct: 129 EDVARNKLIGKHGAKLLEDGD------TVLTHCNAGRLACVDWGTALGVIRS 174
>gnl|CDD|216240 pfam01008, IF-2B, Initiation factor 2 subunit family. This family
includes initiation factor 2B alpha, beta and delta
subunits from eukaryotes, initiation factor 2B subunits
1 and 2 from archaebacteria and some proteins of unknown
function from prokaryotes. Initiation factor 2 binds to
Met-tRNA, GTP and the small ribosomal subunit. Members
of this family have also been characterized as
5-methylthioribose- 1-phosphate isomerases, an enzyme of
the methionine salvage pathway. The crystal structure of
Ypr118w, a non-essential, low-copy number gene product
from Saccharomyces cerevisiae, reveals a dimeric protein
with two domains and a putative active site cleft.
Length = 281
Score = 95.8 bits (239), Expect = 3e-23
Identities = 44/142 (30%), Positives = 71/142 (50%), Gaps = 14/142 (9%)
Query: 145 IKDKQFPDNDSLEKYVGEKLDYLVSARPTAVNMKRAADSVKSSLSEWAKASPVNTVKTRL 204
I+D + P L++ + +++L+SARPTAV++ A D + +SE +S V K L
Sbjct: 20 IQDARTPTVAELKEQLRSAIEFLISARPTAVSLGNAIDRLLRIISELHSSSDVEEAKESL 79
Query: 205 IQLIESMLEKDISDNKAIGRNGAQALIDLNPGVSKLNVLTHCNTGSLATAEYGTALGVIR 264
I+ + +++ + IG A+ + D +LTHCN+ GT LGV+R
Sbjct: 80 IEAADEFIDEIEEARRKIGAIAAELIKD------GDTILTHCNS--------GTVLGVLR 125
Query: 265 SLHGANKIGAAYCTETRPYNQG 286
+ H K TE+RP QG
Sbjct: 126 AAHKEGKRFRVIVTESRPRLQG 147
Score = 45.0 bits (107), Expect = 2e-05
Identities = 32/146 (21%), Positives = 50/146 (34%), Gaps = 63/146 (43%)
Query: 45 QVRGAPAIAIVGCLGLVVDIKDKQFPDNE------------------------------- 73
+VRG+PAIAI GL++ I+D + P
Sbjct: 1 KVRGSPAIAIAALEGLLLVIQDARTPTVAELKEQLRSAIEFLISARPTAVSLGNAIDRLL 60
Query: 74 ------------------LIQLIESMLEKDISDNKAIGRNGAQALIDLNPRVSKLNVLTH 115
LI+ + +++ + IG A+ + D +LTH
Sbjct: 61 RIISELHSSSDVEEAKESLIEAADEFIDEIEEARRKIGAIAAELIKD------GDTILTH 114
Query: 116 CNTGSLATAEYGTALGVIRSLHGANK 141
CN+ GT LGV+R+ H K
Sbjct: 115 CNS--------GTVLGVLRAAHKEGK 132
>gnl|CDD|169386 PRK08334, PRK08334, translation initiation factor IF-2B subunit
beta; Validated.
Length = 356
Score = 80.0 bits (197), Expect = 4e-17
Identities = 44/124 (35%), Positives = 67/124 (54%), Gaps = 8/124 (6%)
Query: 165 DYLVSARPTAVNMKRAADSVKSSLSEWAKASPVNTVKTRLIQLIESMLEKDISDNKAIGR 224
+ L + RPTAVN+ A + +K L E P++ +K +++ + + ++D+ N +G
Sbjct: 94 ETLKNTRPTAVNLFWALNRIKK-LVEEHLEDPLDEIKRLIVEEAQKIADEDVEANLRMGH 152
Query: 225 NGAQALIDLNPGVSKLNVLTHCNTGSLATAEYGTALGVIRSLHGANKIGAAYCTETRPYN 284
GA+ L + NVLTHCN GSLAT GT V+R +H + + ETRP
Sbjct: 153 YGAEVL-------PEGNVLTHCNAGSLATVHLGTVGAVLRVMHKDGTLKLLWVDETRPVL 205
Query: 285 QGAR 288
QGAR
Sbjct: 206 QGAR 209
Score = 78.9 bits (194), Expect = 9e-17
Identities = 56/174 (32%), Positives = 81/174 (46%), Gaps = 41/174 (23%)
Query: 5 QSIIYEKHSLKILDQLLLPHTSKLVDINNVEDAYQAIKSMQVRGAPAIAIVGCLGLVV-- 62
+S+ YE+ + ++DQ LLP K++++ VE+ +AIK+M VRGAPAI GL +
Sbjct: 15 RSVEYEEGKVYMIDQRLLPREFKVIELRTVEEVAEAIKTMTVRGAPAIGAAAAFGLALYA 74
Query: 63 ---DIKDK-QFPD-----------------------NELIQLIESMLEKDISDNKAIGRN 95
K K +F D N + +L+E LE + + K +
Sbjct: 75 ETSKAKTKDEFMDGFYKAYETLKNTRPTAVNLFWALNRIKKLVEEHLEDPLDEIKRLIVE 134
Query: 96 GAQALID----LNPRVSKL--------NVLTHCNTGSLATAEYGTALGVIRSLH 137
AQ + D N R+ NVLTHCN GSLAT GT V+R +H
Sbjct: 135 EAQKIADEDVEANLRMGHYGAEVLPEGNVLTHCNAGSLATVHLGTVGAVLRVMH 188
>gnl|CDD|180547 PRK06371, PRK06371, translation initiation factor IF-2B subunit
alpha; Provisional.
Length = 329
Score = 79.6 bits (196), Expect = 5e-17
Identities = 53/166 (31%), Positives = 77/166 (46%), Gaps = 32/166 (19%)
Query: 2 KSLQSIIYEKHSLKILDQLLLPHTSKLVDINNVEDAYQAIKSMQVRGAPAIAIVGCLGLV 61
K+L+++ YE +K++DQ LP ++ + N +D AIK+M VRGAPAI + GL
Sbjct: 10 KTLKAVWYEDGEVKLIDQRKLPDKIEIFEAKNSDDVAYAIKNMVVRGAPAIGVTAAYGLA 69
Query: 62 VDIKDKQFPDN-------------ELIQLIESMLEKDISDNKA-------------IGRN 95
+ K+ + D +L + I M + N A IG
Sbjct: 70 MASKNGENMDEAVEKIRSTRPTAYDLFKAIRYMNSNEFDMNAARRYAMEIIGRSKKIGEY 129
Query: 96 GAQALIDLNPRVSKLNVLTHCNTGSLATAEYGTALGVIRSLHGANK 141
G + LI R +LTHCN G+LA ++GTAL IR H K
Sbjct: 130 GNE-LIKNGAR-----ILTHCNAGALAVVDWGTALAPIRIAHRNGK 169
Score = 56.4 bits (136), Expect = 4e-09
Identities = 38/129 (29%), Positives = 61/129 (47%), Gaps = 20/129 (15%)
Query: 160 VGEKLDYLVSARPTAVNMKRAADSVKSSLSEWAKASPVNTVKTRLIQLIESMLEKDISDN 219
+ E ++ + S RPTA ++ +A + S+ +N + +++I +
Sbjct: 78 MDEAVEKIRSTRPTAYDLFKAIRYMNSN------EFDMNAARRYAMEIIGR--------S 123
Query: 220 KAIGRNGAQALIDLNPGVSKLNVLTHCNTGSLATAEYGTALGVIRSLHGANKIGAAYCTE 279
K IG G + + + +LTHCN G+LA ++GTAL IR H K + E
Sbjct: 124 KKIGEYGNELIKN------GARILTHCNAGALAVVDWGTALAPIRIAHRNGKNIFVFVDE 177
Query: 280 TRPYNQGAR 288
TRP QGAR
Sbjct: 178 TRPRLQGAR 186
>gnl|CDD|168237 PRK05772, PRK05772, translation initiation factor IF-2B subunit
alpha; Provisional.
Length = 363
Score = 68.2 bits (167), Expect = 4e-13
Identities = 54/180 (30%), Positives = 75/180 (41%), Gaps = 61/180 (33%)
Query: 4 LQSIIYEKHSLKILDQLLLPHTSKLVDINNVEDAYQAIKSMQVRGAPAIAIVGCLGLVV- 62
L II++ ++L +LDQ LLP + VD+ VE+ AI++MQVRGAPAI I G+V+
Sbjct: 16 LLPIIWKDNTLTLLDQSLLPFETVYVDLKTVEEVALAIRNMQVRGAPAIGITAGYGMVLA 75
Query: 63 --------------------DIKDKQFPD---------------------------NELI 75
I D P NELI
Sbjct: 76 LIENNVKTLDDAIRELTRAKTILDSARPTAVNLVWATSRMLNKAKNTVESGNAKSVNELI 135
Query: 76 QLIES----MLEKDISDNKAIGRNGAQALIDLNPRVSKLNVLTHCNTGSLATAEYGTALG 131
+L++ + E++ +G G + L D + VLT CN G LAT GT LG
Sbjct: 136 ELLKVEAKKIFEEEYDAEIQMGLYGLEKLNDGD------TVLTQCNAGGLAT---GTGLG 186
Score = 57.8 bits (140), Expect = 1e-09
Identities = 48/171 (28%), Positives = 75/171 (43%), Gaps = 25/171 (14%)
Query: 123 TAEYGTALGVIRSLHGANKIVDIKDKQFPDNDSLEKYVGEKLDYLVSARPTAVNMKRAAD 182
TA YG L +I N + + +D++ + K L SARPTAVN+ A
Sbjct: 67 TAGYGMVLALI-----ENNVKTL-------DDAIRELTRAK-TILDSARPTAVNLVWATS 113
Query: 183 SVKSSLSEWAKASPVNTVKTRLIQLIES----MLEKDISDNKAIGRNGAQALIDLNPGVS 238
+ + ++ +V LI+L++ + E++ +G G + L D +
Sbjct: 114 RMLNKAKNTVESGNAKSVN-ELIELLKVEAKKIFEEEYDAEIQMGLYGLEKLNDGD---- 168
Query: 239 KLNVLTHCNTGSLATAE-YGTALGVIRSLHGANKIGAAYCTETRPYNQGAR 288
VLT CN G LAT GTAL ++ + ETRP+ QG+R
Sbjct: 169 --TVLTQCNAGGLATGTGLGTALAPVKLAKALGMSVSVIAPETRPWLQGSR 217
>gnl|CDD|236282 PRK08535, PRK08535, translation initiation factor IF-2B subunit
delta; Provisional.
Length = 310
Score = 54.9 bits (133), Expect = 9e-09
Identities = 41/135 (30%), Positives = 58/135 (42%), Gaps = 18/135 (13%)
Query: 152 DNDSLEKYVGEKLDYLVSARPTAVNMKRAADSVKSSLSEWAKASPVNTVKTRLIQLIESM 211
+ + + + L+S RPTAV++ A V S +V R + IES
Sbjct: 44 SPEEFKAEMRAAANILISTRPTAVSLPNAVRYVMRYYSGETVEEARESVIERAEEFIES- 102
Query: 212 LEKDISDNKAIGRNGAQALIDLNPGVSKLNVLTHCNTGSLATAEYGTALGVIRSLHGANK 271
E + IG GA+ + D + ++THCN S A AL VI++ H K
Sbjct: 103 SENAVEK---IGEIGAKRIRDGD------VIMTHCN--SSA------ALSVIKTAHEQGK 145
Query: 272 IGAAYCTETRPYNQG 286
TETRP NQG
Sbjct: 146 DIEVIATETRPRNQG 160
Score = 28.7 bits (65), Expect = 3.4
Identities = 9/20 (45%), Positives = 14/20 (70%)
Query: 34 VEDAYQAIKSMQVRGAPAIA 53
V + + IK+M++RGA IA
Sbjct: 7 VLETAEKIKTMEIRGAGRIA 26
>gnl|CDD|188057 TIGR00511, ribulose_e2b2, ribose-1,5-bisphosphate isomerase, e2b2
family. The delineation of this family was based
originally, in part, on a discussion and
neighbor-joining phylogenetic study by Kyrpides and
Woese of archaeal and other proteins homologous to the
alpha, beta, and delta subunits of eukaryotic initiation
factor 2B (eIF-2B), a five-subunit molecule that
catalyzes GTP recycling for eIF-2. Recently, Sato, et
al. assigned the function ribulose-1,5 bisphosphate
isomerase [Energy metabolism, Other].
Length = 301
Score = 49.3 bits (118), Expect = 7e-07
Identities = 37/120 (30%), Positives = 53/120 (44%), Gaps = 18/120 (15%)
Query: 167 LVSARPTAVNMKRAADSVKSSLSEWAKASPVNTVKTRLIQLIESMLEKDISDNKAIGRNG 226
L+S RPTAV++ A V +S + +V R + I EK IG G
Sbjct: 54 LISTRPTAVSLPNALRYVLKYMSGADVETLRQSVIERADEFINR-SEKAQER---IGEIG 109
Query: 227 AQALIDLNPGVSKLNVLTHCNTGSLATAEYGTALGVIRSLHGANKIGAAYCTETRPYNQG 286
A+ + D + ++THCN+ + AL VI++ K TETRP NQG
Sbjct: 110 AKRIRDGD------VIMTHCNSEA--------ALSVIKTAFEQGKDIEVIVTETRPRNQG 155
Score = 28.1 bits (63), Expect = 4.7
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 34 VEDAYQAIKSMQVRGAPAIA 53
V + + I++M++RGA IA
Sbjct: 2 VLETAEKIRTMEIRGAGRIA 21
>gnl|CDD|224105 COG1184, GCD2, Translation initiation factor 2B subunit, eIF-2B
alpha/beta/delta family [Translation, ribosomal
structure and biogenesis].
Length = 301
Score = 45.8 bits (109), Expect = 1e-05
Identities = 34/142 (23%), Positives = 56/142 (39%), Gaps = 18/142 (12%)
Query: 145 IKDKQFPDNDSLEKYVGEKLDYLVSARPTAVNMKRAADSVKSSLSEWAKASPVNTVKTRL 204
D Q P + L + E + LV ARPTAV++ V S K + ++
Sbjct: 36 ASDSQAPTVEELIDAIRELSETLVKARPTAVSLGNLIRFVLRDSSGGDKENRRQSLIKAA 95
Query: 205 IQLIESMLEKDISDNKAIGRNGAQALIDLNPGVSKLNVLTHCNTGSLATAEYGTALGVIR 264
+ I+ + + + I GA+ + D V +LTH + T L V++
Sbjct: 96 QEFIDRVEKAK----ERIAEIGAERIHD--GDV----ILTHSFS--------KTVLEVLK 137
Query: 265 SLHGANKIGAAYCTETRPYNQG 286
+ K TE+RP +G
Sbjct: 138 TAADRGKRFKVIVTESRPRGEG 159
>gnl|CDD|176728 cd08312, Death_MyD88, Death domain of Myeloid Differentation
primary response protein MyD88. Death Domain (DD) of
Myeloid Differentiation primary response protein 88
(MyD88). MyD88 is an adaptor protein involved in
interleukin-1 receptor (IL-1R)- and Toll-like receptor
(TLR)-induced activation of nuclear factor-kappaB
(NF-kB) and mitogen activated protein kinase pathways
that lead to the induction of proinflammatory cytokines.
It is a key component in the signaling pathway of
pathogen recognition in the innate immune system. MyD88
contains an N-terminal DD and a C-terminal Toll/IL-1
Receptor (TIR) homology domain that mediates interaction
with TLRs and IL-1R. In general, DDs are protein-protein
interaction domains found in a variety of domain
architectures. Their common feature is that they form
homodimers by self-association or heterodimers by
associating with other members of the DD superfamily
including CARD (Caspase activation and recruitment
domain), DED (Death Effector Domain), and PYRIN. They
serve as adaptors in signaling pathways and can recruit
other proteins into signaling complexes.
Length = 79
Score = 28.8 bits (65), Expect = 0.83
Identities = 9/43 (20%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 176 NMKRAADSVKSSLSEWAKASPVNTVKTRLIQLIESMLEKDISD 218
N + + L +W TV L++L+E + +D+
Sbjct: 35 NFETKPSPTEKVLEDWETRPDGATV-GNLLELLEKLERRDVLH 76
>gnl|CDD|107305 cd06310, PBP1_ABC_sugar_binding_like_2, Periplasmic sugar-binding
domain of uncharacterized ABC-type transport systems.
Periplasmic sugar-binding domain of uncharacterized
ABC-type transport systems that share homology with a
family of pentose/hexose sugar-binding proteins of the
type I periplasmic binding protein superfamily, which
consists of two domains connected by a three-stranded
hinge. The substrate specificity of this group is not
known, but it is predicted to be involved in the
transport of sugar-containing molecules and chemotaxis.
Length = 273
Score = 28.7 bits (65), Expect = 3.2
Identities = 16/45 (35%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 207 LIESMLEKDI------SDNKAIGRNGAQALIDLNPGVSKLNVLTH 245
LI+S L DI +DN A G+ A+AL +L K+ V++
Sbjct: 87 LIDSGLNSDIAVSFVATDNVAAGKLAAEALAELLGKKGKVAVISF 131
>gnl|CDD|146574 pfam04013, Methyltrn_RNA_2, Putative SAM-dependent RNA
methyltransferase. This family is likely to be an
S-adenosyl-L-methionine (SAM)-dependent RNA
methyltransferase.
Length = 199
Score = 28.2 bits (63), Expect = 3.5
Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 151 PDNDSLEKYVGEKLDYLVS-ARPTAVNMKRAADSVKSSLSEWAKASPVNTVKTR 203
PD ++ G +L + R A+ +K+A +VK S +W K P V
Sbjct: 60 PDPPRTIRFEGSELKPVSPDERSIAILIKKALRAVKESGKQWRKVLPGIYVSRM 113
>gnl|CDD|173755 cd08215, STKc_Nek, Catalytic domain of the Protein Serine/Threonine
Kinase, Never In Mitosis gene A-related kinase.
Serine/Threonine Kinases (STKs), Never In Mitosis gene A
(NIMA)-related kinase (Nek) family, catalytic (c)
domain. STKs catalyze the transfer of the
gamma-phosphoryl group from ATP to serine/threonine
residues on protein substrates. The Nek family is part
of a larger superfamily that includes the catalytic
domains of other protein STKs, protein tyrosine kinases,
RIO kinases, aminoglycoside phosphotransferase, choline
kinase, and phosphoinositide 3-kinase. The Nek family is
composed of 11 different mammalian members (Nek1-11)
with similarity to the catalytic domain of Aspergillus
nidulans NIMA kinase, the founding member of the Nek
family which was identified in a screen for cell cycle
mutants that were prevented from entering mitosis. Neks
contain a conserved N-terminal catalytic domain and a
more divergent C-terminal regulatory region of various
sizes and structures. They are involved in the
regulation of downstream processes following the
activation of Cdc2, and many of their functions are cell
cycle-related. They play critical roles in microtubule
dynamics during ciliogenesis and mitosis.
Length = 258
Score = 28.2 bits (64), Expect = 4.4
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 6/34 (17%)
Query: 58 LGLVVDIKDKQFP------DNELIQLIESMLEKD 85
L L + I Q+P +EL L+ S+L+KD
Sbjct: 209 LELALKILKGQYPPIPSQYSSELRNLVSSLLQKD 242
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 28.5 bits (64), Expect = 5.9
Identities = 15/75 (20%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 155 SLEKYVGEKLDYLVSARPTAVNMKRAADSVKSS--LSEWAKASPVNTVKTRLIQLIES-- 210
SL +Y+ L + + +++ K A + +S L +W + ++ V L +LI++
Sbjct: 1288 SLLQYINVGLFNALRTKASSLRWKSATEVNYNSEELDDWCREFEISDVDEELEELIQAVK 1347
Query: 211 ---MLEKDISDNKAI 222
+L+ D++ +
Sbjct: 1348 VLQLLKDDLNKLDEL 1362
>gnl|CDD|232982 TIGR00457, asnS, asparaginyl-tRNA synthetase. In a multiple
sequence alignment of representative asparaginyl-tRNA
synthetases (asnS), archaeal/eukaryotic type
aspartyl-tRNA synthetases (aspS_arch), and bacterial
type aspartyl-tRNA synthetases (aspS_bact), there is a
striking similarity between asnS and aspS_arch in gap
pattern and in sequence, and a striking divergence of
aspS_bact. Consequently, a separate model was built for
each of the three groups. This model, asnS, represents
asparaginyl-tRNA synthetases from the three domains of
life. Some species lack this enzyme and charge tRNA(asn)
by misacylation with Asp, followed by transamidation of
Asp to Asn [Protein synthesis, tRNA aminoacylation].
Length = 453
Score = 27.7 bits (62), Expect = 7.8
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 72 NELIQLIESMLEKDISDNKAIGRNGAQALIDLNPRVSKL 110
N+L+QL E++++ I KA+ N +Q L L K
Sbjct: 247 NDLLQLAETLIKYII---KAVLENCSQELKFLEKNFDKD 282
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.314 0.131 0.364
Gapped
Lambda K H
0.267 0.0749 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,030,663
Number of extensions: 1329671
Number of successful extensions: 1075
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1046
Number of HSP's successfully gapped: 48
Length of query: 288
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 192
Effective length of database: 6,679,618
Effective search space: 1282486656
Effective search space used: 1282486656
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 58 (26.1 bits)