RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8681
(521 letters)
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 40.4 bits (94), Expect = 0.002
Identities = 34/159 (21%), Positives = 65/159 (40%), Gaps = 16/159 (10%)
Query: 359 GDEDSVSL-ARRVFERANQALKASSEKEERVMLLEAWKEFEAQ-------HGDDESRAKL 410
DE + E + E E E E E Q GD+ + K+
Sbjct: 742 EDEGEGEAEGKHEVETEGDRKETEHEGETEAEGKEDEDEGEIQAGEDGEMKGDEGAEGKV 801
Query: 411 NSKLPRRAKKRVKTYNDEGVEEGWEEVFDYIFPEDEAAKPNLKLLEKAKAWKKAMEEKQG 470
+ A ++ + + EV D E + N + +AK +K ++ G
Sbjct: 802 EHEGETEAGEKDEHEGQSETQADDTEVKD----ETGEQELNAENQGEAKQDEKGVDGGGG 857
Query: 471 NKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDD 509
+ +G + E EEEE ++E + EEE+E+++E + ++++
Sbjct: 858 S----DGGDSEEEEEEEEEEEEEEEEEEEEEEEEEENEE 892
Score = 39.6 bits (92), Expect = 0.005
Identities = 25/136 (18%), Positives = 54/136 (39%), Gaps = 3/136 (2%)
Query: 383 EKEERVMLLEAWKEFEAQHGDDESRAKLNSKLPRRAKKRVKTYNDEGVEEGWEEVFDYIF 442
E + + E E E + +DE + + + + + E E ++
Sbjct: 758 EGDRKETEHEGETEAEGKEDEDEGEIQAGEDGEMKGDEGAEGKVEHEGETEAGEKDEHEG 817
Query: 443 PEDEAAKPNLKLLEKAKAWKKAMEEKQGN-KIGEEGANKENEEEERDKERDREEEDEKKD 501
+ A E + + E QG K E+G + + D E + EEE+E+++
Sbjct: 818 QSETQADDTEVKDETGEQ--ELNAENQGEAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEE 875
Query: 502 ERDRDSDDERDDREED 517
E + + ++E ++ E +
Sbjct: 876 EEEEEEEEEEEEEENE 891
Score = 34.6 bits (79), Expect = 0.13
Identities = 19/87 (21%), Positives = 39/87 (44%)
Query: 19 EAKERDLEIVPPVEEGWEEVFDYIFPEDEAAKPNLKLLEKAKAWKKAMEEKQGNKIGEEG 78
E + + + + E + N + +AK +K ++ G+ G+
Sbjct: 805 GETEAGEKDEHEGQSETQADDTEVKDETGEQELNAENQGEAKQDEKGVDGGGGSDGGDSE 864
Query: 79 ANKENEEEERDKERDREEEDERKDEGD 105
+E EEEE ++E + EEE+E ++E +
Sbjct: 865 EEEEEEEEEEEEEEEEEEEEEEEEENE 891
Score = 31.9 bits (72), Expect = 0.93
Identities = 13/46 (28%), Positives = 29/46 (63%)
Query: 64 KAMEEKQGNKIGEEGANKENEEEERDKERDREEEDERKDEGDRDSD 109
+A ++++G G ++EEEE ++E + EEE+E ++E + + +
Sbjct: 844 EAKQDEKGVDGGGGSDGGDSEEEEEEEEEEEEEEEEEEEEEEEEEE 889
Score = 31.9 bits (72), Expect = 0.98
Identities = 39/161 (24%), Positives = 64/161 (39%), Gaps = 12/161 (7%)
Query: 355 EMSSGDEDSVSLARRVFERANQALKASSEKEERVMLLEAWKEFEAQHGDDESRAKLNSKL 414
S G+ + + E +A +A + E +E E EA+ +DE +
Sbjct: 679 NESEGEIPAERKGEQEGEGEIEAKEADHKGETEAEEVEHEGETEAEGTEDEGEIETG--- 735
Query: 415 PRRAKKRVKTYNDEGVEEGWEEVFDYIFPEDEAAKPNLKLLEKAKAWKKAMEEKQGNKIG 474
+ EG EG EV E E + + + +A K E++ + G
Sbjct: 736 ---EEGEEVEDEGEGEAEGKHEV------ETEGDRKETEHEGETEAEGKEDEDEGEIQAG 786
Query: 475 EEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDRE 515
E+G K +E E E + E E +KDE + S+ + DD E
Sbjct: 787 EDGEMKGDEGAEGKVEHEGETEAGEKDEHEGQSETQADDTE 827
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 38.9 bits (90), Expect = 0.007
Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 56 LEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDERKDEGDR 106
L +K KK E+ K E K EE ER+KE+++E E ER+ E +R
Sbjct: 572 LASSKLAKK--REEAVEKAKREAEQKAREEREREKEKEKEREREREREAER 620
Score = 36.6 bits (84), Expect = 0.038
Identities = 19/51 (37%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 455 LEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDR 505
L +K KK E+ K E K EE ER+KE+++E E E++ E +R
Sbjct: 572 LASSKLAKK--REEAVEKAKREAEQKAREEREREKEKEKEREREREREAER 620
Score = 36.2 bits (83), Expect = 0.043
Identities = 18/43 (41%), Positives = 29/43 (67%), Gaps = 1/43 (2%)
Query: 476 EGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDS 518
E A +E E++ R+ ER+RE+E EK+ ER+R+ + ER + S
Sbjct: 586 EKAKREAEQKARE-EREREKEKEKEREREREREAERAAKASSS 627
Score = 33.5 bits (76), Expect = 0.33
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 475 EEGANKENEEEERDKERDREEEDEKKDERDRDSDDERD 512
EE K E E+ +RE E EK+ ER+R+ + E +
Sbjct: 582 EEAVEKAKREAEQKAREEREREKEKEKEREREREREAE 619
Score = 32.0 bits (72), Expect = 0.94
Identities = 22/66 (33%), Positives = 35/66 (53%), Gaps = 13/66 (19%)
Query: 448 AKPNLKLLEKAK--AWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDR 505
AK + +EKAK A +KA EE++ K E+E+++ER+RE E E+ +
Sbjct: 578 AKKREEAVEKAKREAEQKAREEREREK-----------EKEKEREREREREAERAAKASS 626
Query: 506 DSDDER 511
S + R
Sbjct: 627 SSHESR 632
Score = 31.2 bits (70), Expect = 1.6
Identities = 13/34 (38%), Positives = 26/34 (76%), Gaps = 1/34 (2%)
Query: 77 EGANKENEEEER-DKERDREEEDERKDEGDRDSD 109
E A +E E++ R ++ER++E+E ER+ E +R+++
Sbjct: 586 EKAKREAEQKAREEREREKEKEKEREREREREAE 619
>gnl|CDD|215521 PLN02967, PLN02967, kinase.
Length = 581
Score = 37.7 bits (87), Expect = 0.015
Identities = 32/130 (24%), Positives = 55/130 (42%), Gaps = 13/130 (10%)
Query: 402 GDDESRAKLN---SKLPRRAKKRVKTYNDEGVEEGWEEV--FDYIFPEDEAAKPNLKLLE 456
DE+ A ++ +RA K+ E +EEG E V D ++ P +
Sbjct: 61 EPDENGAVSKKKPTRSVKRATKKTVVEISEPLEEGSELVVNEDAALDKESKKTPRRTRRK 120
Query: 457 KAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKK--------DERDRDSD 508
A A EEK K+ + K+ +E+ D+ + E D ++ +E + + D
Sbjct: 121 AAAASSDVEEEKTEKKVRKRRKVKKMDEDVEDQGSESEVSDVEESEFVTSLENESEEELD 180
Query: 509 DERDDREEDS 518
E+DD E+ S
Sbjct: 181 LEKDDGEDIS 190
>gnl|CDD|214642 smart00386, HAT, HAT (Half-A-TPR) repeats. Present in several
RNA-binding proteins. Structurally and sequentially
thought to be similar to TPRs.
Length = 33
Score = 32.9 bits (76), Expect = 0.016
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 290 GDMERARAIYELAISQPRLDMPELVWKAYIDFE 322
GD+ERAR IYE A+ + + +W Y +FE
Sbjct: 1 GDIERARKIYERALEKFPKSVE--LWLKYAEFE 31
Score = 31.4 bits (72), Expect = 0.068
Identities = 12/33 (36%), Positives = 23/33 (69%), Gaps = 1/33 (3%)
Query: 326 GERDKVRELHERLLERTV-HVKVWMNYAQFEMS 357
G+ ++ R+++ER LE+ V++W+ YA+FE
Sbjct: 1 GDIERARKIYERALEKFPKSVELWLKYAEFEER 33
Score = 30.2 bits (69), Expect = 0.14
Identities = 14/30 (46%), Positives = 21/30 (70%), Gaps = 3/30 (10%)
Query: 129 ARKVYERAVEFFGEENLDEKLFIAFAKFEE 158
ARK+YERA+E F +L++ +A+FEE
Sbjct: 6 ARKIYERALEKFP---KSVELWLKYAEFEE 32
>gnl|CDD|219838 pfam08432, DUF1742, Fungal protein of unknown function (DUF1742).
This is a family of fungal proteins of unknown function.
Length = 182
Score = 36.2 bits (84), Expect = 0.017
Identities = 21/79 (26%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 443 PEDEAAKPNLKLL-EKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKD 501
E AK K L E+ + KK EEKQ K ++ + K+ ++++ K+ ++++ EKKD
Sbjct: 55 AEYTEAKKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKD 114
Query: 502 ERDRDSDDERDDREEDSIN 520
E++ + E +
Sbjct: 115 EKEAEDKLEDLTKSYSETL 133
Score = 34.7 bits (80), Expect = 0.053
Identities = 21/73 (28%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 44 PEDEAAKPNLKLL-EKAKAWKKAMEEKQG---NKIGEEGANKENEEEERDKERDREEEDE 99
E AK K L E+ + KK EEKQ K + ++++++ DK+ D+ E+ +
Sbjct: 55 AEYTEAKKKKKELAEEIEKVKKEYEEKQKWKWKKKKSKKKKDKDKDKKDDKKDDKSEKKD 114
Query: 100 RKDEGDRDSDTTY 112
K+ D+ D T
Sbjct: 115 EKEAEDKLEDLTK 127
>gnl|CDD|227438 COG5107, RNA14, Pre-mRNA 3'-end processing (cleavage and
polyadenylation) factor [RNA processing and
modification].
Length = 660
Score = 35.4 bits (81), Expect = 0.080
Identities = 31/170 (18%), Positives = 63/170 (37%), Gaps = 38/170 (22%)
Query: 235 QYEEEVNSNPNNYDAWFDYLRLLEDEGNADLIRETYERAIANIPPTKFAELESLLGDMER 294
+ E + NP N ++F ++ LE + + D RE YE+ +
Sbjct: 30 RLRERIKDNPTNILSYFQLIQYLETQESMDAEREMYEQ-------------------LSS 70
Query: 295 ARAIYELAISQPRLDMPELVWKAYIDFEVGQGERDKVRELHERLLERTVHVKVWMNYAQF 354
I E A W+ Y+ E+ + + V L R L++++++ +WM Y ++
Sbjct: 71 PFPIMEHA------------WRLYMSGELARKDFRSVESLFGRCLKKSLNLDLWMLYLEY 118
Query: 355 ---EMSSGDEDSVSLARRVFE----RANQALKASSEKEERVMLLEAWKEF 397
+ +E A ++ + +E + LE +E
Sbjct: 119 IRRVNNLITGQKRFKIYEAYEFVLGCAIFEPQSENYWDEYGLFLEYIEEL 168
Score = 31.1 bits (70), Expect = 1.5
Identities = 14/53 (26%), Positives = 26/53 (49%)
Query: 289 LGDMERARAIYELAISQPRLDMPELVWKAYIDFEVGQGERDKVRELHERLLER 341
+ D E ARA++E ++ + + ++ I++E G + V L ER E
Sbjct: 479 INDEENARALFETSVERLEKTQLKRIYDKMIEYESMVGSLNNVYSLEERFREL 531
>gnl|CDD|234059 TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat
lipoprotein. This protein family occurs in strictly
within a subset of Gram-negative bacterial species with
the proposed PEP-CTERM/exosortase system, analogous to
the LPXTG/sortase system common in Gram-positive
bacteria. This protein occurs in a species if and only
if a transmembrane histidine kinase (TIGR02916) and a
DNA-binding response regulator (TIGR02915) also occur.
The present of tetratricopeptide repeats (TPR) suggests
protein-protein interaction, possibly for the regulation
of PEP-CTERM protein expression, since many PEP-CTERM
proteins in these genomes are preceded by a proposed DNA
binding site for the response regulator.
Length = 899
Score = 35.1 bits (81), Expect = 0.11
Identities = 19/79 (24%), Positives = 34/79 (43%), Gaps = 5/79 (6%)
Query: 230 SKRKFQYEEEVNSNPNNYDAWFDYLRLLEDEGNADLIRETYERAIANIPP-----TKFAE 284
+K + +E+ ++ P+ + A + R+ EGN D + +E+ + P A
Sbjct: 482 AKAREAFEKALSIEPDFFPAAANLARIDIQEGNPDDAIQRFEKVLTIDPKNLRAILALAG 541
Query: 285 LESLLGDMERARAIYELAI 303
L G+ E A A E A
Sbjct: 542 LYLRTGNEEEAVAWLEKAA 560
Score = 29.3 bits (66), Expect = 5.7
Identities = 25/132 (18%), Positives = 49/132 (37%), Gaps = 12/132 (9%)
Query: 288 LLGDMERARAIYELAISQPRLDMPELVWKAYIDFEVGQGERDKVRELHERLLERTV-HVK 346
LG +E A+ YE A++ + + A + + + D+ R L + +L +V
Sbjct: 137 GLGQLELAQKSYEQALAIDPRSLYAKLGLAQL--ALAENRFDEARALIDEVLTADPGNVD 194
Query: 347 VWMNYAQFEMSSGD----EDSVSLARRVFERANQALKASSEKEERVMLLEAWKEFEAQHG 402
+ +S G+ + A + L A + +L+EA + EA+
Sbjct: 195 ALLLKGDLLLSLGNIELALAAYRKAIALRPNNIAVLLALA-----TILIEAGEFEEAEKH 249
Query: 403 DDESRAKLNSKL 414
D K +
Sbjct: 250 ADALLKKAPNSP 261
>gnl|CDD|217476 pfam03286, Pox_Ag35, Pox virus Ag35 surface protein.
Length = 198
Score = 34.0 bits (78), Expect = 0.11
Identities = 24/90 (26%), Positives = 38/90 (42%), Gaps = 2/90 (2%)
Query: 432 EGWEEVFDYIFPED-EAAKPNLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKE 490
E ++V D IFPED E P ++ +K K+ K +E +E ++ E D +
Sbjct: 29 ESVDKVRDDIFPEDIEIPSPKQPKKKRPTTPRKPATTKKSKKKDKEKLTEEEKKPESDDD 88
Query: 491 RDREEE-DEKKDERDRDSDDERDDREEDSI 519
+ E E D +E DS + I
Sbjct: 89 KTEENENDPDNNEESGDSQESASANSLSDI 118
Score = 32.4 bits (74), Expect = 0.40
Identities = 22/83 (26%), Positives = 37/83 (44%), Gaps = 4/83 (4%)
Query: 33 EGWEEVFDYIFPED-EAAKPNLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKE 91
E ++V D IFPED E P ++ +K K+ K +E +E ++ E D +
Sbjct: 29 ESVDKVRDDIFPEDIEIPSPKQPKKKRPTTPRKPATTKKSKKKDKEKLTEEEKKPESDDD 88
Query: 92 RDREEE---DERKDEGDRDSDTT 111
+ E E D ++ GD +
Sbjct: 89 KTEENENDPDNNEESGDSQESAS 111
>gnl|CDD|238112 cd00189, TPR, Tetratricopeptide repeat domain; typically contains
34 amino acids
[WLF]-X(2)-[LIM]-[GAS]-X(2)-[YLF]-X(8)-[ASE]-X(3)-[FYL]-
X(2)-[ASL]-X(4)-[PKE] is the consensus sequence; found
in a variety of organisms including bacteria,
cyanobacteria, yeast, fungi, plants, and humans in
various subcellular locations; involved in a variety of
functions including protein-protein interactions, but
common features in the interaction partners have not
been defined; involved in chaperone, cell-cycle,
transciption, and protein transport complexes; the
number of TPR motifs varies among proteins (1,3-11,13
15,16,19); 5-6 tandem repeats generate a right-handed
helical structure with an amphipathic channel that is
thought to accomodate an alpha-helix of a target
protein; it has been proposed that TPR proteins
preferably interact with WD-40 repeat proteins, but in
many instances several TPR-proteins seem to aggregate to
multi-protein complexes; examples of TPR-proteins
include, Cdc16p, Cdc23p and Cdc27p components of the
cyclosome/APC, the Pex5p/Pas10p receptor for peroxisomal
targeting signals, the Tom70p co-receptor for
mitochondrial targeting signals, Ser/Thr phosphatase 5C
and the p110 subunit of O-GlcNAc transferase; three
copies of the repeat are present here.
Length = 100
Score = 32.0 bits (73), Expect = 0.16
Identities = 21/100 (21%), Positives = 43/100 (43%), Gaps = 10/100 (10%)
Query: 180 FQYEEHERARVIYKYALDHIPKDRTAEIYKAYTIHEKKYGDRAGIEDVIVSKRKFQYEEE 239
++ +++ A Y+ AL+ P + A A ++ + A +ED YE+
Sbjct: 11 YKLGDYDEALEYYEKALELDPDNADAYYNLAAAYYKLGKYEEA-LED---------YEKA 60
Query: 240 VNSNPNNYDAWFDYLRLLEDEGNADLIRETYERAIANIPP 279
+ +P+N A+++ G + E YE+A+ P
Sbjct: 61 LELDPDNAKAYYNLGLAYYKLGKYEEALEAYEKALELDPN 100
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein. CDC45 is an essential gene
required for initiation of DNA replication in S.
cerevisiae, forming a complex with MCM5/CDC46.
Homologues of CDC45 have been identified in human, mouse
and smut fungus among others.
Length = 583
Score = 34.2 bits (79), Expect = 0.19
Identities = 17/55 (30%), Positives = 28/55 (50%)
Query: 465 MEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDSI 519
EE Q ++ E+++ D+E D E+E+ K E D D DD+ DD + +
Sbjct: 107 EEELQDEPRYDDAYRDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDDIATR 161
Score = 31.9 bits (73), Expect = 0.96
Identities = 14/57 (24%), Positives = 28/57 (49%)
Query: 461 WKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREED 517
+ E++ + EE+ D + + +EEDE+ + + D DD+ DD ++D
Sbjct: 101 FDDGDIEEELQDEPRYDDAYRDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDD 157
Score = 28.8 bits (65), Expect = 9.2
Identities = 9/37 (24%), Positives = 21/37 (56%)
Query: 475 EEGANKENEEEERDKERDREEEDEKKDERDRDSDDER 511
++ + +EE+E + + +E+D+ D+ D + ER
Sbjct: 127 DDDDEESDEEDEESSKSEDDEDDDDDDDDDDIATRER 163
Score = 28.8 bits (65), Expect = 9.3
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 475 EEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREED 517
EE + + E +E D+E + E+DE D+ D D D +R +
Sbjct: 124 EEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDDIATRERSLE 166
>gnl|CDD|219834 pfam08424, NRDE-2, NRDE-2, necessary for RNA interference. This is
a family of eukaryotic proteins. Eukaryotic cells
express a wide variety of endogenous small regulatory
RNAs that regulate heterochromatin formation,
developmental timing, defence against parasitic nucleic
acids, and genome rearrangement. Many small regulatory
RNAs are thought to function in nuclei, and in plants
and fungi small interfering (si)RNAs associate with
nascent transcripts and direct chromatin and/or DNA
modifications. This family protein, NRDE-2, is required
for small interfering (si)RNA-mediated silencing in
nuclei. NRDE-2 associates with the Argonaute protein
NRDE-3 within nuclei and is recruited by NRDE-3/siRNA
complexes to nascent transcripts that have been targeted
by RNA interference, RNAi, the process whereby
double-stranded RNA (dsRNA) directs the
sequence-specific degradation of mRNA.
Length = 324
Score = 33.1 bits (76), Expect = 0.30
Identities = 38/163 (23%), Positives = 67/163 (41%), Gaps = 26/163 (15%)
Query: 229 VSKRKFQYEEEVNSNPNNYDAWFDYLRLLEDEGNADLIRETYERAIANIPPTKFAELESL 288
+ KR + +V NP + DAW + +R E+ L+R + R+ AE + L
Sbjct: 1 ILKRNAELNRKVRENPEDIDAWIELIRFQEE-----LLRLSRRRS-------TKAERKQL 48
Query: 289 LGDMERARAIYELAI-SQPRLDMPELV---WKAYIDFEVGQGERDKVRELHERLLERTVH 344
E+ +I E A+ P D L+ + + D++ + E++L+
Sbjct: 49 A---EKKLSILEKALKHNP--DSERLLLGLLEEGEKVW----DTDELLKRWEKVLKENPG 99
Query: 345 -VKVWMNYAQFEMSSGDEDSVSLARRVFERANQALKASSEKEE 386
K+W Y F S S R+ +E+ +ALKA+
Sbjct: 100 SPKLWRKYLDFRQGDFSTFSYSKVRKTYEKCLRALKAALNGTI 142
>gnl|CDD|219408 pfam07423, DUF1510, Protein of unknown function (DUF1510). This
family consists of several hypothetical bacterial
proteins of around 200 residues in length. The function
of this family is unknown.
Length = 214
Score = 32.8 bits (75), Expect = 0.30
Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 2/77 (2%)
Query: 442 FPEDEAAKPNLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKD 501
P D+AA + K ++ E ++ + +E AN E++E++ D E++ EE +E+ +
Sbjct: 39 SPSDQAAADEQE--AKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENE 96
Query: 502 ERDRDSDDERDDREEDS 518
E D +S DE + E+
Sbjct: 97 EEDEESSDENEKETEEK 113
Score = 28.5 bits (64), Expect = 6.6
Identities = 19/67 (28%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 43 FPEDEAAKPNLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDERKD 102
P D+AA + K ++ E ++ + +E AN E++E++ D E++ EE +E +
Sbjct: 39 SPSDQAAADEQE--AKKSDDQETAEIEEVKEEEKEAANSEDKEDKGDAEKEDEESEEENE 96
Query: 103 EGDRDSD 109
E D +S
Sbjct: 97 EEDEESS 103
>gnl|CDD|237171 PRK12678, PRK12678, transcription termination factor Rho;
Provisional.
Length = 672
Score = 33.3 bits (77), Expect = 0.32
Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 464 AMEEKQGNKIGEEGANKEN--EEEERDKERDREEEDEKKDERDRDSDDERDDREEDS 518
+ + + GE G +E + ++RD+ RE+ D +++ RD D R R
Sbjct: 178 REDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRD 234
Score = 31.8 bits (73), Expect = 0.98
Identities = 10/52 (19%), Positives = 20/52 (38%)
Query: 466 EEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREED 517
+ G+ ++ + E RD + ++ RDR D+RE+
Sbjct: 196 RGRDGDDRDRRDRREQGDRREERGRRDGGDRRGRRRRRDRRDARGDDNREDR 247
Score = 30.6 bits (70), Expect = 2.4
Identities = 16/52 (30%), Positives = 23/52 (44%)
Query: 466 EEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREED 517
EE++ + E ER + REE D+RDR E+ DR E+
Sbjct: 166 EEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRREE 217
Score = 30.6 bits (70), Expect = 2.6
Identities = 9/45 (20%), Positives = 19/45 (42%)
Query: 474 GEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDS 518
++E+ + E ++ E+ +D DRD D R+ +
Sbjct: 172 RRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQGDRRE 216
Score = 29.9 bits (68), Expect = 4.4
Identities = 13/76 (17%), Positives = 32/76 (42%)
Query: 443 PEDEAAKPNLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDE 502
P EA + E+ + ++ + ++ E + EER ++ D + +++++
Sbjct: 152 PATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREERGRDGDDRDRRDRREQ 211
Query: 503 RDRDSDDERDDREEDS 518
DR + R D +
Sbjct: 212 GDRREERGRRDGGDRR 227
Score = 29.5 bits (67), Expect = 5.0
Identities = 9/53 (16%), Positives = 22/53 (41%)
Query: 466 EEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDS 518
+ +G + A + E ++ERD +++R +++ R E+
Sbjct: 144 KAGEGGEQPATEARADAAERTEEEERDERRRRGDREDRQAEAERGERGRREER 196
>gnl|CDD|220759 pfam10446, DUF2457, Protein of unknown function (DUF2457). This is
a family of uncharacterized proteins.
Length = 449
Score = 33.4 bits (76), Expect = 0.33
Identities = 17/38 (44%), Positives = 26/38 (68%)
Query: 480 KENEEEERDKERDREEEDEKKDERDRDSDDERDDREED 517
KE EEE ++E D EE+D+ D+ D D DD+ DD +++
Sbjct: 43 KEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDE 80
Score = 33.0 bits (75), Expect = 0.43
Identities = 18/52 (34%), Positives = 33/52 (63%)
Query: 467 EKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDS 518
E K+G+E + EEE+ D+E D +++DE +D+ D D D++ +D ++D
Sbjct: 35 ENAIRKLGKEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDD 86
Score = 31.5 bits (71), Expect = 1.1
Identities = 17/59 (28%), Positives = 34/59 (57%), Gaps = 6/59 (10%)
Query: 455 LEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDD 513
++K A +K +E EE A +E +++E D + D +E+++ D+ D + D++ DD
Sbjct: 32 MKKENAIRKLGKEA------EEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDD 84
Score = 29.2 bits (65), Expect = 6.8
Identities = 14/62 (22%), Positives = 34/62 (54%)
Query: 457 KAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREE 516
+A ++AMEE+ ++ ++ + E+E+++ D + + +E+++ D D D E
Sbjct: 42 GKEAEEEAMEEEDDDEEDDDDDDDEDEDDDDDDDDEDDEDEDDDDSTLHDDSSADDGNET 101
Query: 517 DS 518
D+
Sbjct: 102 DN 103
>gnl|CDD|185618 PTZ00438, PTZ00438, gamete antigen 27/25-like protein; Provisional.
Length = 374
Score = 33.1 bits (75), Expect = 0.38
Identities = 32/109 (29%), Positives = 51/109 (46%), Gaps = 5/109 (4%)
Query: 415 PRRAKKRVKTYNDEGVEEGWEEVFDYIFPEDEAAKPNLKLLEKAKAWKKAMEEKQGNKIG 474
P ++ + + N E E+ E DYI E+ +A N+ + K+ + E +G I
Sbjct: 37 PSNTREEIISVNYEPEEQDLSEACDYIAIEEYSACGNVASIANDKSDNENDVELEGLNII 96
Query: 475 -----EEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDS 518
E G KE EE+E +E + EE E +E D +D D E++S
Sbjct: 97 VKNEEERGTQKEEEEDEDVEEIEEVEEVEVVEEEYDDDEDSEKDDEKES 145
>gnl|CDD|117592 pfam09026, Cenp-B_dimeris, Centromere protein B dimerisation
domain. The centromere protein B (CENP-B) dimerisation
domain is composed of two alpha-helices, which are
folded into an antiparallel configuration. Dimerisation
of CENP-B is mediated by this domain, in which monomers
dimerise to form a symmetrical, antiparallel, four-helix
bundle structure with a large hydrophobic patch in which
23 residues of one monomer form van der Waals contacts
with the other monomer. This CENP-B dimer configuration
may be suitable for capturing two distant CENP-B boxes
during centromeric heterochromatin formation.
Length = 101
Score = 30.5 bits (68), Expect = 0.55
Identities = 16/32 (50%), Positives = 22/32 (68%)
Query: 484 EEERDKERDREEEDEKKDERDRDSDDERDDRE 515
EE+ D + D EE+D+ +DE D D DD+ DD E
Sbjct: 9 EEDSDSDSDEEEDDDDEDEEDDDEDDDEDDDE 40
Score = 28.2 bits (62), Expect = 3.5
Identities = 14/31 (45%), Positives = 22/31 (70%)
Query: 474 GEEGANKENEEEERDKERDREEEDEKKDERD 504
GEE ++ +++EEE D + D E++DE DE D
Sbjct: 8 GEEDSDSDSDEEEDDDDEDEEDDDEDDDEDD 38
Score = 27.8 bits (61), Expect = 5.4
Identities = 14/31 (45%), Positives = 22/31 (70%)
Query: 75 GEEGANKENEEEERDKERDREEEDERKDEGD 105
GEE ++ +++EEE D + D E++DE DE D
Sbjct: 8 GEEDSDSDSDEEEDDDDEDEEDDDEDDDEDD 38
Score = 27.4 bits (60), Expect = 7.7
Identities = 16/38 (42%), Positives = 24/38 (63%), Gaps = 1/38 (2%)
Query: 484 EEERDKERDREEEDEKKDERDRDSDDERDDREEDSINV 521
E E D + D +EE++ DE D + DDE DD ++D + V
Sbjct: 7 EGEEDSDSDSDEEEDDDDE-DEEDDDEDDDEDDDEVPV 43
>gnl|CDD|218333 pfam04931, DNA_pol_phi, DNA polymerase phi. This family includes
the fifth essential DNA polymerase in yeast EC:2.7.7.7.
Pol5p is localised exclusively to the nucleolus and
binds near or at the enhancer region of rRNA-encoding
DNA repeating units.
Length = 784
Score = 32.5 bits (74), Expect = 0.59
Identities = 13/61 (21%), Positives = 29/61 (47%)
Query: 457 KAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREE 516
KA K ++ + +E +E +++E + E + E E + + + +DE++D E
Sbjct: 633 KADENKSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAE 692
Query: 517 D 517
Sbjct: 693 A 693
Score = 29.5 bits (66), Expect = 5.1
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 9/62 (14%)
Query: 463 KAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKK------DERDRDSDDERDDREE 516
KA E K ++ EG E E+E+ +E D +E++ + + D E D++E+
Sbjct: 633 KADENKSRHQQLFEG---EEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQED 689
Query: 517 DS 518
D+
Sbjct: 690 DA 691
Score = 29.1 bits (65), Expect = 6.6
Identities = 11/60 (18%), Positives = 24/60 (40%)
Query: 451 NLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDE 510
+ EE+ + + E +++ E D E + E + E +E +++ D E
Sbjct: 633 KADENKSRHQQLFEGEEEDEDDLEETDDDEDECEAIEDSESESESDGEDGEEDEQEDDAE 692
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 32.2 bits (74), Expect = 0.70
Identities = 17/59 (28%), Positives = 30/59 (50%)
Query: 446 EAAKPNLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERD 504
K K E+ K KK + + EE ++ EEE+ ++E + EEE E+++E+
Sbjct: 415 IVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKK 473
Score = 31.8 bits (73), Expect = 0.84
Identities = 14/60 (23%), Positives = 33/60 (55%)
Query: 453 KLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERD 512
+ + K ++ +EK+ + +E EEE+ KE ++EEE+E+ +E + ++++
Sbjct: 415 IVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKKK 474
Score = 31.0 bits (71), Expect = 1.5
Identities = 17/59 (28%), Positives = 28/59 (47%)
Query: 47 EAAKPNLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDERKDEGD 105
K K E+ K KK + + EE ++ EEE+ ++E + EEE E ++E
Sbjct: 415 IVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEEEEKK 473
Score = 31.0 bits (71), Expect = 1.7
Identities = 18/69 (26%), Positives = 44/69 (63%)
Query: 446 EAAKPNLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDR 505
+A K K++EKA+ ++ ++++ K +E EEEE++K+ + +EE+E++ E ++
Sbjct: 407 KATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEK 466
Query: 506 DSDDERDDR 514
+ ++E+ +
Sbjct: 467 EEEEEKKKK 475
Score = 29.9 bits (68), Expect = 3.7
Identities = 11/66 (16%), Positives = 39/66 (59%)
Query: 453 KLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERD 512
K ++K + E++ + ++ + +EEE ++E++++EE+++++E + + + E +
Sbjct: 410 KKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEEKEEE 469
Query: 513 DREEDS 518
+ ++
Sbjct: 470 EEKKKK 475
Score = 29.1 bits (66), Expect = 6.5
Identities = 20/64 (31%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 456 EKAKAWKKAMEEKQGNKIGEEGANKENEEEER-DKERDREEEDEKKDERDRDSDDERDDR 514
+KA K + EK K EE K+ + KE + EEE EKK+E + ++E ++
Sbjct: 406 KKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEEEAEEE 465
Query: 515 EEDS 518
+E+
Sbjct: 466 KEEE 469
Score = 28.7 bits (65), Expect = 8.2
Identities = 13/55 (23%), Positives = 26/55 (47%)
Query: 467 EKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDSINV 521
+K KI + E + EE KE+ ++ KK E + + + E+ + E++
Sbjct: 406 KKATKKIKKIVEKAEKKREEEKKEKKKKAFAGKKKEEEEEEEKEKKEEEKEEEEE 460
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown].
Length = 434
Score = 31.7 bits (72), Expect = 1.1
Identities = 15/65 (23%), Positives = 35/65 (53%)
Query: 444 EDEAAKPNLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDER 503
++ + N KL + K + +E ++ E A +E ++E ++++ +E+ DE K++R
Sbjct: 368 QELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKEKR 427
Query: 504 DRDSD 508
+D
Sbjct: 428 QKDER 432
Score = 29.8 bits (67), Expect = 3.5
Identities = 11/67 (16%), Positives = 33/67 (49%)
Query: 36 EEVFDYIFPEDEAAKPNLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDRE 95
+E+ + + L ++ + E K + ++ N++ ++E+ D+++++
Sbjct: 368 QELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKEKR 427
Query: 96 EEDERKD 102
++DERK
Sbjct: 428 QKDERKK 434
Score = 29.8 bits (67), Expect = 4.2
Identities = 10/67 (14%), Positives = 33/67 (49%)
Query: 435 EEVFDYIFPEDEAAKPNLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDRE 494
+E+ + + L ++ + E K + ++ N++ ++E+ D+++++
Sbjct: 368 QELLKEYNKKLQDYTKKLGEVKDETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKEKR 427
Query: 495 EEDEKKD 501
++DE+K
Sbjct: 428 QKDERKK 434
Score = 29.8 bits (67), Expect = 4.3
Identities = 14/56 (25%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 462 KKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREED 517
+ ++ K +E E E + +E+ ++EE+EKK + D D E+ ++E
Sbjct: 379 QDYTKKLGEVK--DETDASEEAEAKAKEEKLKQEENEKKQKEQADEDKEKRQKDER 432
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 31.5 bits (71), Expect = 1.3
Identities = 15/72 (20%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 445 DEAAKPNLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERD 504
DE + +L E+ K+ +++ + + + +E NK E+++R ++ D EE + D
Sbjct: 3909 DEPNEEDLLETEQ-KSNEQSAANNESDLVSKEDDNKALEDKDRQEKEDEEEMSDDVGIDD 3967
Query: 505 RDSDDERDDREE 516
D +++ +
Sbjct: 3968 EIQPDIQENNSQ 3979
Score = 31.1 bits (70), Expect = 2.1
Identities = 28/103 (27%), Positives = 49/103 (47%), Gaps = 18/103 (17%)
Query: 426 NDEGVEEGWEEVFDYIFPEDEAAKPNLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEE 485
++E ++ EEV D PED + N KL ++ + +E +Q + E+ A N E
Sbjct: 3881 SEEENQDLDEEVND--IPEDLSNSLNEKLWDE-PNEEDLLETEQKSN--EQSA--ANNES 3933
Query: 486 ERDKERD----------REEEDEKKDERDRDSDDE-RDDREED 517
+ + D +E+EDE++ D DDE + D +E+
Sbjct: 3934 DLVSKEDDNKALEDKDRQEKEDEEEMSDDVGIDDEIQPDIQEN 3976
>gnl|CDD|217940 pfam04177, TAP42, TAP42-like family. The TOR signalling pathway
activates a cell-growth program in response to
nutrients. TIP41 (pfam04176) interacts with TAP42 and
negatively regulates the TOR signaling pathway.
Length = 335
Score = 31.1 bits (71), Expect = 1.4
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 466 EEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDD 513
E K+G + G EE + + D EE+D+++ + R D+ +DD
Sbjct: 287 EMKRGGVP-QGGGEAAASAEEEEDDEDDEEDDDEETLKARAWDEFKDD 333
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes Pseudomonas denitrificans CobT gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There are
apparently a number of variations on these two pathways,
where the major differences seem to be concerned with
the process of ring contraction. Confusion regarding the
functions of enzymes found in the aerobic vs. anaerobic
pathways has arisen because nonhomologous genes in these
different pathways were given the same gene symbols.
Thus, cobT in the aerobic pathway (P. denitrificans) is
not a homolog of cobT in the anaerobic pathway (S.
typhimurium). It should be noted that E. coli
synthesizes cobalamin only when it is supplied with the
precursor cobinamide, which is a complex intermediate.
Additionally, all E. coli cobalamin synthesis genes
(cobU, cobS and cobT) were named after their Salmonella
typhimurium homologs which function in the anaerobic
cobalamin synthesis pathway. This model describes the
aerobic cobalamin pathway Pseudomonas denitrificans CobT
gene product, which is a cobalt chelatase subunit, with
a MW ~70 kDa. The aerobic pathway cobalt chelatase is a
heterotrimeric, ATP-dependent enzyme that catalyzes
cobalt insertion during cobalamin biosynthesis. The
other two subunits are the P. denitrificans CobS
(TIGR01650) and CobN (pfam02514 CobN/Magnesium
Chelatase) proteins. To avoid potential confusion with
the nonhomologous Salmonella typhimurium/E.coli cobT
gene product, the P. denitrificans gene symbol is not
used in the name of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 600
Score = 31.1 bits (70), Expect = 1.6
Identities = 15/53 (28%), Positives = 26/53 (49%)
Query: 466 EEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDS 518
E +Q + EG +E + + DRE E +++ D DD D+ ++DS
Sbjct: 222 ENEQEEQGEGEGEGQEGSAPQESEATDRESESGEEEMVQSDQDDLPDESDDDS 274
>gnl|CDD|188167 TIGR01780, SSADH, succinate-semialdehyde dehydrogenase. Succinic
semialdehyde dehydrogenase is one of three enzymes
constituting 4-aminobutyrate (GABA) degradation in both
prokaryotes and eukaryotes, catalyzing the
(NAD(P)+)-dependent catabolism reaction of succinic
semialdehyde to succinate for metabolism by the citric
acid cycle. The EC number depends on the cofactor:
1.2.1.24 for NAD only, 1.2.1.79 for NADP only, and
1.2.1.16 if both can be used. In Escherichia coli,
succinic semialdehyde dehydrogenase is located in an
unidirectionally transcribed gene cluster encoding
enzymes for GABA degradation and is suggested to be
cotranscribed with succinic semialdehyde transaminase
from a common promoter upstream of SSADH. Similar gene
arrangements can be found in characterized Ralstonia
eutropha and the genome analysis of Bacillus subtilis.
Prokaryotic succinic semialdehyde dehydrogenases
(1.2.1.16) share high sequence homology to characterized
succinic semialdehyde dehydrogenases from rat and human
(1.2.1.24), exhibiting conservation of proposed cofactor
binding residues, and putative active sites (G-237 &
G-242, C-293 & G-259 respectively of rat SSADH).
Eukaryotic SSADH enzymes exclusively utilize NAD+ as a
cofactor, exhibiting little to no NADP+ activity. While
a NADP+ preference has been detected in prokaryotes in
addition to both NADP+- and NAD+-dependencies as in
E.coli, Pseudomonas, and Klebsiella pneumoniae. The
function of this alternative SSADH currently is unknown,
but has been suggested to play a possible role in
4-hydroxyphenylacetic degradation. Just outside the
scope of this model, are several sequences belonging to
clades scoring between trusted and noise. These
sequences may be actual SSADH enzymes, but lack
sufficiently close characterized homologs to make a
definitive assignment at this time. SSADH enzyme belongs
to the aldehyde dehydrogenase family (pfam00171),
sharing a common evolutionary origin and enzymatic
mechanism with lactaldehyde dehydrogenase. Like in
lactaldehyde dehydrogenase and succinate semialdehyde
dehydrogenase, the mammalian catalytic glutamic acid and
cysteine residues are conserved in all the enzymes of
this family (PS00687, PS00070) [Central intermediary
metabolism, Other].
Length = 448
Score = 30.9 bits (70), Expect = 1.6
Identities = 12/47 (25%), Positives = 17/47 (36%), Gaps = 2/47 (4%)
Query: 363 SVSLARRVFERANQALKASSE--KEERVMLLEAWKEFEAQHGDDESR 407
V A +A K +ER LL W ++ DD +R
Sbjct: 17 GVDETEAAIRAAYEAFKTWRATTAKERSSLLRKWYNLMMENKDDLAR 63
>gnl|CDD|217348 pfam03064, U79_P34, HSV U79 / HCMV P34. This family represents
herpes virus protein U79 and cytomegalovirus early
phosphoprotein P34 (UL112).
Length = 238
Score = 30.2 bits (68), Expect = 2.0
Identities = 15/62 (24%), Positives = 35/62 (56%), Gaps = 2/62 (3%)
Query: 451 NLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDE-KKDERDRDSDD 509
++K EK + +A+ K+ + + + K+ +E+ R ++ + +ED KK E R +D+
Sbjct: 136 DVKNAEKFEKECRALSRKKSDDEHRKRSGKQ-KEKRRVEDSQKHKEDRRKKQEEKRRNDE 194
Query: 510 ER 511
++
Sbjct: 195 DK 196
Score = 28.7 bits (64), Expect = 7.6
Identities = 15/60 (25%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 52 NLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDERK-DEGDRDSDT 110
++K EK + +A+ K+ + + + K+ +E+ R ++ + +ED RK E R +D
Sbjct: 136 DVKNAEKFEKECRALSRKKSDDEHRKRSGKQ-KEKRRVEDSQKHKEDRRKKQEEKRRNDE 194
>gnl|CDD|237047 PRK12298, obgE, GTPase CgtA; Reviewed.
Length = 390
Score = 30.6 bits (70), Expect = 2.1
Identities = 10/43 (23%), Positives = 24/43 (55%)
Query: 475 EEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREED 517
EE +E EE E ++ + +D +++ + +++ DD ++D
Sbjct: 333 EENPREEAEEAEAPEKVEFMWDDYHREQLEEVEEEDDDDWDDD 375
>gnl|CDD|219655 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 30.3 bits (69), Expect = 2.2
Identities = 14/47 (29%), Positives = 24/47 (51%)
Query: 459 KAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDR 505
+ KA EE++ + E+ K+ EE E + EE K +E++R
Sbjct: 270 EKILKAAEEERQEEAQEKKEEKKKEEREAKLAKLSPEEQRKLEEKER 316
>gnl|CDD|218107 pfam04484, DUF566, Family of unknown function (DUF566). Family of
related proteins that is plant specific.
Length = 313
Score = 30.3 bits (68), Expect = 2.3
Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 2/57 (3%)
Query: 362 DSVSLARRVFERANQALKASSEKEERVMLLEAWKEFEAQHGD--DESRAKLNSKLPR 416
+SV++ R +R Q LK +S + ++ LE W + E H + L + R
Sbjct: 196 NSVAMKRIKLQRLRQELKLNSVLKSQMSYLEEWSDLERDHSSSLSGAIEALKASTLR 252
>gnl|CDD|233503 TIGR01642, U2AF_lg, U2 snRNP auxilliary factor, large subunit,
splicing factor. These splicing factors consist of an
N-terminal arginine-rich low complexity domain followed
by three tandem RNA recognition motifs (pfam00076). The
well-characterized members of this family are auxilliary
components of the U2 small nuclear ribonuclearprotein
splicing factor (U2AF). These proteins are closely
related to the CC1-like subfamily of splicing factors
(TIGR01622). Members of this subfamily are found in
plants, metazoa and fungi.
Length = 509
Score = 30.6 bits (69), Expect = 2.3
Identities = 11/37 (29%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 482 NEEEERDKERDREEEDEKKDERDRD-SDDERDDREED 517
+EE +R++E+ R + ++ ER R S D R+
Sbjct: 2 DEEPDREREKSRGRDRDRSSERPRRRSRDRSRFRDRH 38
Score = 29.5 bits (66), Expect = 4.7
Identities = 15/32 (46%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 487 RDKERDREEEDEKKDERDRDSDDERDDREEDS 518
RD+E DRE EK RDRD ER R
Sbjct: 1 RDEEPDRER--EKSRGRDRDRSSERPRRRSRD 30
Score = 29.5 bits (66), Expect = 5.2
Identities = 12/58 (20%), Positives = 21/58 (36%), Gaps = 1/58 (1%)
Query: 461 WKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDS 518
EK + + + + RD+ R R+ ++ R+ RD R DS
Sbjct: 4 EPDREREKSRGRDRDRSSER-PRRRSRDRSRFRDRHRRSRERSYREDSRPRDRRRYDS 60
>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha
subunit (TFIIF-alpha). Transcription initiation factor
IIF, alpha subunit (TFIIF-alpha) or RNA polymerase
II-associating protein 74 (RAP74) is the large subunit
of transcription factor IIF (TFIIF), which is essential
for accurate initiation and stimulates elongation by RNA
polymerase II.
Length = 528
Score = 30.3 bits (68), Expect = 2.5
Identities = 29/143 (20%), Positives = 56/143 (39%), Gaps = 29/143 (20%)
Query: 402 GDDESRAKLNSKLPRRAKKRVKTYNDEG-------------VEEGWEEVFDYIFPEDEAA 448
G+D K K + AK + K +D+ ++G +E + + D +A
Sbjct: 233 GEDGDEEKSKKKKKKLAKNKKKLDDDKKGKRGGDDDADEYDSDDGDDEGREEDYISDSSA 292
Query: 449 KPNLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEED----------- 497
N + + K + E +I ++ ++E+EEE+ ++E ++
Sbjct: 293 SGND---PEEREDKLSPEIPAKPEIEQDEDSEESEEEKNEEEGGLSKKGKKLKKLKGKKN 349
Query: 498 --EKKDERDRDSDDERDDREEDS 518
+K D D D+ D EDS
Sbjct: 350 GLDKDDSDSGDDSDDSDIDGEDS 372
>gnl|CDD|218421 pfam05086, Dicty_REP, Dictyostelium (Slime Mold) REP protein. This
family consists of REP proteins from Dictyostelium
(Slime molds). REP protein is likely involved in
transcription regulation and control of DNA replication,
specifically amplification of plasmid at low copy
numbers. The formation of homomultimers may be required
for their regulatory activity.
Length = 910
Score = 30.6 bits (69), Expect = 2.8
Identities = 13/41 (31%), Positives = 21/41 (51%)
Query: 477 GANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREED 517
N + EE + +E ED+ DE + +DE +D +ED
Sbjct: 869 ELNDLTDLEEYLISQFQENEDDDADEDEDQDEDEDEDEDED 909
>gnl|CDD|217257 pfam02867, Ribonuc_red_lgC, Ribonucleotide reductase, barrel
domain.
Length = 516
Score = 29.8 bits (68), Expect = 3.5
Identities = 20/84 (23%), Positives = 34/84 (40%), Gaps = 11/84 (13%)
Query: 349 MNYAQFEMSSG----DEDSVSLARRVFER-ANQALKASSE-KEERVMLLEAWKEFEA-QH 401
M A G E++ LA +FE ALKAS+E +E+ + FE ++
Sbjct: 291 MGLADALAKLGIPYDSEEARELADEIFETIYYYALKASNELAKEK----GPFPGFEGSKY 346
Query: 402 GDDESRAKLNSKLPRRAKKRVKTY 425
E A + ++ +K +
Sbjct: 347 AKGEFHAIPLREDWEELREDIKKH 370
>gnl|CDD|240329 PTZ00248, PTZ00248, eukaryotic translation initiation factor 2
subunit 1; Provisional.
Length = 319
Score = 29.6 bits (67), Expect = 3.6
Identities = 23/73 (31%), Positives = 44/73 (60%), Gaps = 6/73 (8%)
Query: 452 LKLLEKA-KAWKKAMEEKQGN-KIGEE----GANKENEEEERDKERDREEEDEKKDERDR 505
++++ A +A K+ +++K G+ K+ E G ++E+ EE +K + EEED+ + D
Sbjct: 242 MEIIGAALEAIKEVIKKKGGDFKVKGEPEVVGGDEEDLEELLEKAEEEEEEDDYSESEDE 301
Query: 506 DSDDERDDREEDS 518
D +DE ++ EED
Sbjct: 302 DEEDEDEEEEEDD 314
Score = 28.5 bits (64), Expect = 9.7
Identities = 11/45 (24%), Positives = 28/45 (62%)
Query: 466 EEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDE 510
+E+ ++ E+ +E E++ + E + EE++++++E D D D+
Sbjct: 275 DEEDLEELLEKAEEEEEEDDYSESEDEDEEDEDEEEEEDDDEGDK 319
>gnl|CDD|237629 PRK14160, PRK14160, heat shock protein GrpE; Provisional.
Length = 211
Score = 29.3 bits (66), Expect = 4.3
Identities = 16/52 (30%), Positives = 29/52 (55%)
Query: 466 EEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREED 517
+ K N + EN+EE++ KE D E E+ +K+E DS++ + + E+
Sbjct: 7 DAKHENMEEDCCKENENKEEDKGKEEDLEFEEIEKEEIIEDSEESNEVKIEE 58
>gnl|CDD|219355 pfam07267, Nucleo_P87, Nucleopolyhedrovirus capsid protein P87.
This family consists of several Nucleopolyhedrovirus
capsid protein P87 sequences. P87 is expressed late in
infection and concentrated in infected cell nuclei.
Length = 606
Score = 29.9 bits (67), Expect = 4.3
Identities = 19/84 (22%), Positives = 37/84 (44%), Gaps = 4/84 (4%)
Query: 27 IVPPVEEGWEEVFDYIFPEDEAA---KPNLKLLEKAKAWKKAMEEKQGNKIGEEGANKEN 83
P WEE+ FP D A P+ + + ++ + E ++ E+
Sbjct: 316 PKPEPIYTWEELLRERFPSDLFAISSLPDSDSEASDSGPTRKRKRRRVPPL-PEYSSDED 374
Query: 84 EEEERDKERDREEEDERKDEGDRD 107
E++ + E D E+E +R+ E D++
Sbjct: 375 EDDSDEDEVDYEKERKRRREEDKN 398
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 29.9 bits (67), Expect = 4.5
Identities = 13/45 (28%), Positives = 30/45 (66%)
Query: 474 GEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDS 518
+E +E+ EEE ++E + EEE+++ +E + + ++E ++ E D+
Sbjct: 436 SQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADN 480
Score = 29.5 bits (66), Expect = 5.6
Identities = 16/56 (28%), Positives = 34/56 (60%)
Query: 463 KAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDS 518
A +E + + EE +E EEEE ++E + EE +++++E + ++D+ ++ E S
Sbjct: 434 MASQESEEEESVEEEEEEEEEEEEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGS 489
>gnl|CDD|185603 PTZ00415, PTZ00415, transmission-blocking target antigen s230;
Provisional.
Length = 2849
Score = 30.0 bits (67), Expect = 4.6
Identities = 14/42 (33%), Positives = 29/42 (69%)
Query: 476 EGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREED 517
+ +++ +E++ D+E D EEE+E+++ + D +DE D+ ED
Sbjct: 154 DDDDEDEDEDDDDEEDDEEEEEEEEEIKGFDDEDEEDEGGED 195
>gnl|CDD|217861 pfam04050, Upf2, Up-frameshift suppressor 2. Transcripts
harbouring premature signals for translation termination
are recognised and rapidly degraded by eukaryotic cells
through a pathway known as nonsense-mediated mRNA decay.
In Saccharomyces cerevisiae, three trans-acting factors
(Upf1 to Upf3) are required for nonsense-mediated mRNA
decay.
Length = 171
Score = 28.9 bits (65), Expect = 4.7
Identities = 15/41 (36%), Positives = 23/41 (56%)
Query: 481 ENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDSINV 521
E +EE +++ D E DE++ + D DE D EE+ I V
Sbjct: 11 EEDEELPEEDEDDESSDEEEVDLPDDEQDEESDSEEEQIFV 51
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 29.3 bits (66), Expect = 4.7
Identities = 20/82 (24%), Positives = 34/82 (41%), Gaps = 7/82 (8%)
Query: 444 EDEAAKPNLK--LLE-----KAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEE 496
EDE K +L+ L E K+K K E + +N+ +E+++ + E R+
Sbjct: 51 EDELRKRDLRAELEEAERAHKSKKENKLAIEDADKSTNLDASNEGDEDDDEEDEIKRKRI 110
Query: 497 DEKKDERDRDSDDERDDREEDS 518
+E D D D D +
Sbjct: 111 EEDARNSDADDSDSSSDSDSSD 132
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 29.6 bits (67), Expect = 5.1
Identities = 13/44 (29%), Positives = 28/44 (63%)
Query: 475 EEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDS 518
E+G + E+EE++ D + EE+ + DE + + D++ DD +++
Sbjct: 327 EDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEE 370
Score = 29.2 bits (66), Expect = 5.9
Identities = 13/53 (24%), Positives = 26/53 (49%)
Query: 466 EEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDS 518
+ N +G E EEE+ + D E++D+ +E + D D ++ +E+
Sbjct: 308 PDDDDNFGLGQGEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEED 360
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 29.7 bits (67), Expect = 5.1
Identities = 11/39 (28%), Positives = 20/39 (51%)
Query: 474 GEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERD 512
+ E EE+E ++E + E+E K+ D + +E D
Sbjct: 384 ANTERDDEEEEDEEEEEEEDEDEGPSKEHSDDEEFEEDD 422
>gnl|CDD|216317 pfam01131, Topoisom_bac, DNA topoisomerase. This subfamily of
topoisomerase is divided on the basis that these enzymes
preferentially relax negatively supercoiled DNA, from a
5' phospho- tyrosine linkage in the enzyme-DNA covalent
intermediate and has high affinity for single stranded
DNA.
Length = 365
Score = 29.1 bits (66), Expect = 5.3
Identities = 14/41 (34%), Positives = 21/41 (51%)
Query: 30 PVEEGWEEVFDYIFPEDEAAKPNLKLLEKAKAWKKAMEEKQ 70
+E GW++V+ EDE P LK E+ +EEK+
Sbjct: 230 LLEPGWKKVYPDEKDEDEEPLPELKEGEELDVKDVELEEKK 270
Score = 28.7 bits (65), Expect = 7.8
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 430 VEEGWEEVFDYIFPEDEAAKPNLKLLEKAKAWKKAMEEKQ 469
+E GW++V+ EDE P LK E+ +EEK+
Sbjct: 231 LEPGWKKVYPDEKDEDEEPLPELKEGEELDVKDVELEEKK 270
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.7 bits (66), Expect = 5.5
Identities = 33/151 (21%), Positives = 70/151 (46%), Gaps = 2/151 (1%)
Query: 367 ARRVFERANQALKASSEKEERVMLLEAWKEFEAQHGDDESRAKLNSKLPRRAKKRVKTYN 426
A++ E + + E+E+++ EA K EA+ +E + K K+ +
Sbjct: 1586 AKKAEEARIEEVMKLYEEEKKMKAEEAKKAEEAKIKAEELKKAEEEKKKVEQLKKKEAEE 1645
Query: 427 DEGVEEGWEEVFDYIFPEDEAAKPNLKLLEKAKAWKKAMEEKQGNKIGEEGANKENEEEE 486
+ EE + + E AK + +KA+ KKA E+++ K E + E ++
Sbjct: 1646 KKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEK--KAAEALKKEAEEAKK 1703
Query: 487 RDKERDREEEDEKKDERDRDSDDERDDREED 517
++ + +E E++KK E + +++E + E+
Sbjct: 1704 AEELKKKEAEEKKKAEELKKAEEENKIKAEE 1734
>gnl|CDD|215601 PLN03142, PLN03142, Probable chromatin-remodeling complex ATPase
chain; Provisional.
Length = 1033
Score = 29.4 bits (66), Expect = 5.5
Identities = 11/57 (19%), Positives = 24/57 (42%)
Query: 465 MEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDSINV 521
EE+ + EE +E E R D ++++ ++ D D +D+ + +
Sbjct: 1 EEEQVNTQANEEEDEEELEAVARSAGSDSDDDEVPAEDEDEDEEDDEEAESPAKAEI 57
>gnl|CDD|183610 PRK12585, PRK12585, putative monovalent cation/H+ antiporter
subunit G; Reviewed.
Length = 197
Score = 28.9 bits (64), Expect = 5.6
Identities = 15/67 (22%), Positives = 40/67 (59%), Gaps = 3/67 (4%)
Query: 455 LEKAKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDR---DSDDER 511
+EKA+ ++ +EE+ + EE ++ ++EE+++ER+ + +E+ D+ + + D+
Sbjct: 128 IEKARQEREELEERMEWERREEKIDEREDQEEQEREREEQTIEEQSDDSEHEIIEQDESE 187
Query: 512 DDREEDS 518
+ ++D
Sbjct: 188 TESDDDK 194
>gnl|CDD|215774 pfam00183, HSP90, Hsp90 protein.
Length = 529
Score = 29.4 bits (66), Expect = 5.7
Identities = 14/40 (35%), Positives = 24/40 (60%)
Query: 478 ANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREED 517
KE E+E D+E + E+E++K++E +E D EE+
Sbjct: 27 VEKEVEKEVPDEEEEEEKEEKKEEEEKTTDKEEEVDEEEE 66
>gnl|CDD|226920 COG4547, CobT, Cobalamin biosynthesis protein CobT
(nicotinate-mononucleotide:5, 6-dimethylbenzimidazole
phosphoribosyltransferase) [Coenzyme metabolism].
Length = 620
Score = 29.4 bits (66), Expect = 5.7
Identities = 13/45 (28%), Positives = 22/45 (48%)
Query: 474 GEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDS 518
EE + EE+ + D E E+ + D + D E D+ +ED+
Sbjct: 251 REESEGSDESEEDEAEATDGEGEEGEMDAAEASEDSESDESDEDT 295
>gnl|CDD|221175 pfam11705, RNA_pol_3_Rpc31, DNA-directed RNA polymerase III subunit
Rpc31. RNA polymerase III contains seventeen subunits
in yeasts and in human cells. Twelve of these are akin
to RNA polymerase I or II and the other five are RNA pol
III-specific, and form the functionally distinct groups
(i) Rpc31-Rpc34-Rpc82, and (ii) Rpc37-Rpc53. Rpc31,
Rpc34 and Rpc82 form a cluster of enzyme-specific
subunits that contribute to transcription initiation in
S.cerevisiae and H.sapiens. There is evidence that these
subunits are anchored at or near the N-terminal Zn-fold
of Rpc1, itself prolonged by a highly conserved but RNA
polymerase III-specific domain.
Length = 221
Score = 28.6 bits (64), Expect = 6.6
Identities = 14/52 (26%), Positives = 30/52 (57%)
Query: 466 EEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREED 517
+ + + E+ + E+ +++ EEE+E+++E D D DD+ DD ++D
Sbjct: 148 DIDEKLSMLEKKLKELEAEDVDEEDEKDEEEEEEEEEEDEDFDDDDDDDDDD 199
>gnl|CDD|218556 pfam05327, RRN3, RNA polymerase I specific transcription initiation
factor RRN3. This family consists of several eukaryotic
proteins which are homologous to the yeast RRN3 protein.
RRN3 is one of the RRN genes specifically required for
the transcription of rDNA by RNA polymerase I (Pol I) in
Saccharomyces cerevisiae.
Length = 554
Score = 29.2 bits (66), Expect = 6.6
Identities = 11/36 (30%), Positives = 21/36 (58%)
Query: 481 ENEEEERDKERDREEEDEKKDERDRDSDDERDDREE 516
+ ++EE ++ E++D++ D D D DDE + E
Sbjct: 224 DIDDEEEERVLADEDDDDEDDMFDMDDDDEEESDPE 259
Score = 28.8 bits (65), Expect = 9.3
Identities = 10/41 (24%), Positives = 23/41 (56%)
Query: 481 ENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDSINV 521
++EEEER + +++++ + D D ++E D E + +
Sbjct: 226 DDEEEERVLADEDDDDEDDMFDMDDDDEEESDPEVERTSTI 266
>gnl|CDD|223879 COG0809, QueA,
S-adenosylmethionine:tRNA-ribosyltransferase-isomerase
(queuine synthetase) [Translation, ribosomal structure
and biogenesis].
Length = 348
Score = 28.7 bits (65), Expect = 7.1
Identities = 23/104 (22%), Positives = 42/104 (40%), Gaps = 23/104 (22%)
Query: 135 RAVEFFGEENLDEKLFIAFAKFEEGQREKYGDR----AGIEDVIVSKR-------KFQYE 183
VE E LD+ ++A K +R K GD G++ ++ + +F YE
Sbjct: 77 GKVEVLLERRLDDNRWLALIK--PSKRLKAGDEIYFGDGLKATVLERLEHGLRLLEFDYE 134
Query: 184 EHERAR-VIYKYALDHIP-----KDRTAEIYKAY--TIHEKKYG 219
++ KY +P K + E+ + T++ K+ G
Sbjct: 135 GIFSLLELLEKYG--EMPLPPYIKRKLDELDRDRYQTVYAKEPG 176
>gnl|CDD|153177 cd04905, ACT_CM-PDT, C-terminal ACT domain of the bifunctional
chorismate mutase-prephenate dehydratase (CM-PDT) enzyme
and the prephenate dehydratase (PDT) enzyme. The
C-terminal ACT domain of the bifunctional chorismate
mutase-prephenate dehydratase (CM-PDT) enzyme and the
prephenate dehydratase (PDT) enzyme, found in plants,
fungi, bacteria, and archaea. The P-protein of E. coli
(CM-PDT, PheA) catalyzes the conversion of chorismate to
prephenate and then the decarboxylation and dehydration
to form phenylpyruvate. These are the first two steps in
the biosynthesis of L-Phe and L-Tyr via the shikimate
pathway in microorganisms and plants. The E. coli
P-protein (CM-PDT) has three domains with an N-terminal
domain with chorismate mutase activity, a middle domain
with prephenate dehydratase activity, and an ACT
regulatory C-terminal domain. The prephenate dehydratase
enzyme has a PDT and ACT domain. The ACT domain is
essential to bring about the negative allosteric
regulation by L-Phe binding. L-Phe binds with positive
cooperativity; with this binding, there is a shift in
the protein to less active tetrameric and higher
oligomeric forms from a more active dimeric form.
Members of this CD belong to the superfamily of ACT
regulatory domains.
Length = 80
Score = 26.7 bits (60), Expect = 7.2
Identities = 15/34 (44%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 318 YIDFEVGQGERDKVRELHERLLERTVHVKVWMNY 351
+IDFE G E V E E L T VKV +Y
Sbjct: 47 FIDFE-GHIEDPNVAEALEELKRLTEFVKVLGSY 79
>gnl|CDD|205609 pfam13431, TPR_17, Tetratricopeptide repeat.
Length = 34
Score = 25.6 bits (57), Expect = 8.0
Identities = 10/33 (30%), Positives = 19/33 (57%)
Query: 236 YEEEVNSNPNNYDAWFDYLRLLEDEGNADLIRE 268
YE+ + +PNN +A+++ LL + G D +
Sbjct: 2 YEKALELDPNNAEAYYNLALLLLNLGQYDEALQ 34
>gnl|CDD|217783 pfam03896, TRAP_alpha, Translocon-associated protein (TRAP), alpha
subunit. The alpha-subunit of the TRAP complex (TRAP
alpha) is a single-spanning membrane protein of the
endoplasmic reticulum (ER) which is found in proximity
of nascent polypeptide chains translocating across the
membrane.
Length = 281
Score = 28.6 bits (64), Expect = 8.1
Identities = 14/50 (28%), Positives = 21/50 (42%)
Query: 470 GNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREEDSI 519
G + +EE D D +EEDE E D + E ++ EE +
Sbjct: 24 GKGPFASAQDLTEDEEAEDDVVDEDEEDEAVVEEDENELTEEEEDEEGEV 73
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 28.8 bits (65), Expect = 9.3
Identities = 18/124 (14%), Positives = 40/124 (32%)
Query: 398 EAQHGDDESRAKLNSKLPRRAKKRVKTYNDEGVEEGWEEVFDYIFPEDEAAKPNLKLLEK 457
A+ ++ AK K + K+ + N ++ V D + +
Sbjct: 82 AAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQADDDDDDDDDDD 141
Query: 458 AKAWKKAMEEKQGNKIGEEGANKENEEEERDKERDREEEDEKKDERDRDSDDERDDREED 517
++ + ++ + ++E+E KE E+ D+ D DD R+
Sbjct: 142 LDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDFVWDEDDSEALRQAR 201
Query: 518 SINV 521
Sbjct: 202 KDAK 205
>gnl|CDD|214663 smart00437, TOP1Ac, Bacterial DNA topoisomerase I DNA-binding
domain. Bacterial DNA topoisomerase I and III,
Eukaryotic DNA topoisomeraes III, reverse gyrase alpha
subunit.
Length = 259
Score = 28.4 bits (64), Expect = 9.3
Identities = 16/66 (24%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 8 EIQITAEQLLREAKERDLEIVPPVEEGWEEVFDYIFPEDEAAKPNLKLLEKAKAWKKAME 67
++ I +AK + L + +GW +V+ E+E P LK ++ K + +E
Sbjct: 146 KVTIKIGGEKFKAKGKTL-----LFDGWLKVYPEEKKEEEIELPTLKKGDELKVEEVEVE 200
Query: 68 EKQGNK 73
EK+
Sbjct: 201 EKETKP 206
>gnl|CDD|227480 COG5151, SSL1, RNA polymerase II transcription
initiation/nucleotide excision repair factor TFIIH,
subunit SSL1 [Transcription / DNA replication,
recombination, and repair].
Length = 421
Score = 28.4 bits (63), Expect = 9.5
Identities = 17/62 (27%), Positives = 29/62 (46%), Gaps = 5/62 (8%)
Query: 465 MEEKQGNKIGEEGANKENEEEERDKERDREEEDEKK-----DERDRDSDDERDDREEDSI 519
M E Q + ++ +++ ++ R K R R+ +D K E R DD DD+E +
Sbjct: 1 MNENQKSFDSDKSESEDEQKNGRVKVRSRKTDDMNKGYSWEQEYKRSWDDVNDDKEGSLV 60
Query: 520 NV 521
V
Sbjct: 61 GV 62
>gnl|CDD|115196 pfam06524, NOA36, NOA36 protein. This family consists of several
NOA36 proteins which contain 29 highly conserved
cysteine residues. The function of this protein is
unknown.
Length = 314
Score = 28.4 bits (63), Expect = 9.5
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 75 GEEGANKENEEEERDKERDREEEDERKDEGDRDSD 109
+N +EEE+ D + + + +D + GD D D
Sbjct: 277 EGSSSNDYDEEEDGDDDDNEDNDDTNTNHGDEDCD 311
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
0.310 0.131 0.364
Gapped
Lambda K H
0.267 0.0788 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,205,052
Number of extensions: 2985856
Number of successful extensions: 9206
Number of sequences better than 10.0: 1
Number of HSP's gapped: 6946
Number of HSP's successfully gapped: 747
Length of query: 521
Length of database: 10,937,602
Length adjustment: 101
Effective length of query: 420
Effective length of database: 6,457,848
Effective search space: 2712296160
Effective search space used: 2712296160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 61 (27.2 bits)