RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13906
(914 letters)
>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like.
Members of this group possess KH domains in a tandem
arrangement. Most members, similar to the poly(C)
binding proteins (PCBPs) and Nova, containing three KH
domains, with the first and second domains, which are
represented here, in tandem arrangement, followed by a
large spacer region, with the third domain near the
C-terminal end of the protein. The poly(C) binding
proteins (PCBPs) can be divided into two groups, hnRNPs
K/J and the alphaCPs, which share a triple KH domain
configuration and poly(C) binding specificity. They
play roles in mRNA stabilization, translational
activation, and translational silencing. Nova-1 and
Nova-2 are nuclear RNA-binding proteins that regulate
splicing. This group also contains plant proteins that
seem to have two tandem repeat arrrangements, like Hen4,
a protein that plays a role in AGAMOUS (AG) pre-mRNA
processing and important step in plant development. In
general, KH binds single-stranded RNA or DNA. It is
found in a wide variety of proteins including ribosomal
proteins, transcription factors and post-transcriptional
modifiers of mRNA.
Length = 65
Score = 89.5 bits (223), Expect = 8e-22
Identities = 38/65 (58%), Positives = 46/65 (70%)
Query: 81 QLRLIVPASQCGSIIGKGGSQIKTIRETSGASVYVASDMLPNSTEREVNIKGVPDAVTQA 140
LRL+VP+SQ GSIIGKGGS IK IRE +GA + V+ +LP STER V I G P AV +A
Sbjct: 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKA 60
Query: 141 IYQIC 145
+ I
Sbjct: 61 LLLIL 65
Score = 89.5 bits (223), Expect = 8e-22
Identities = 38/65 (58%), Positives = 46/65 (70%)
Query: 526 QLRLIVPASQCGSIIGKGGSQIKTIRETSGASVYVASDMLPNSTEREVNIKGVPDAVTQA 585
LRL+VP+SQ GSIIGKGGS IK IRE +GA + V+ +LP STER V I G P AV +A
Sbjct: 1 TLRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKA 60
Query: 586 IYQIC 590
+ I
Sbjct: 61 LLLIL 65
Score = 71.7 bits (177), Expect = 1e-15
Identities = 26/64 (40%), Positives = 42/64 (65%), Gaps = 3/64 (4%)
Query: 442 MRHIMQGKEVGSIIGKSGETVKKLREESGSKIYISDS---STPERIVTVIGSMDSLFRAF 498
+R ++ + GSIIGK G T+K++REE+G+KI +S S + ER+VT+ G ++ +A
Sbjct: 2 LRLLVPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKAL 61
Query: 499 SLIT 502
LI
Sbjct: 62 LLIL 65
Score = 69.8 bits (172), Expect = 6e-15
Identities = 25/60 (41%), Positives = 39/60 (65%), Gaps = 3/60 (5%)
Query: 1 MQGKEVGSIIGKSGETVKKLREESGSKIYISDS---STPERIVTVIGSMDSLFRAFSLIT 57
+ + GSIIGK G T+K++REE+G+KI +S S + ER+VT+ G ++ +A LI
Sbjct: 6 VPSSQAGSIIGKGGSTIKEIREETGAKIRVSKSVLPGSTERVVTISGKPSAVQKALLLIL 65
Score = 63.6 bits (156), Expect = 8e-13
Identities = 28/61 (45%), Positives = 40/61 (65%), Gaps = 2/61 (3%)
Query: 268 VPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTGTPDAIALAQYL 327
VP+ G++IGKGG+ I EIR+ +GA IR+SKS S +R +T++G P A+ A L
Sbjct: 6 VPSSQAGSIIGKGGSTIKEIREETGAKIRVSKS--VLPGSTERVVTISGKPSAVQKALLL 63
Query: 328 I 328
I
Sbjct: 64 I 64
Score = 63.6 bits (156), Expect = 8e-13
Identities = 28/61 (45%), Positives = 40/61 (65%), Gaps = 2/61 (3%)
Query: 713 VPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTGTPDAIALAQYL 772
VP+ G++IGKGG+ I EIR+ +GA IR+SKS S +R +T++G P A+ A L
Sbjct: 6 VPSSQAGSIIGKGGSTIKEIREETGAKIRVSKS--VLPGSTERVVTISGKPSAVQKALLL 63
Query: 773 I 773
I
Sbjct: 64 I 64
>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA. There are two different KH domains that belong
to different protein folds, but they share a single KH
motif. The KH motif is folded into a beta alpha alpha
beta unit. In addition to the core, type II KH domains
(e.g. ribosomal protein S3) include N-terminal extension
and type I KH domains (e.g. hnRNP K) contain C-terminal
extension.
Length = 64
Score = 70.7 bits (174), Expect = 3e-15
Identities = 29/66 (43%), Positives = 45/66 (68%), Gaps = 3/66 (4%)
Query: 263 TKEMTVPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTGTPDAIA 322
T+ + VP+ L+G +IGKGG+ I EIR+ +GA I+I + S +R +T+TGTP+A+
Sbjct: 1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKI---PDSGSGSEERIVTITGTPEAVE 57
Query: 323 LAQYLI 328
A+ LI
Sbjct: 58 KAKELI 63
Score = 70.7 bits (174), Expect = 3e-15
Identities = 29/66 (43%), Positives = 45/66 (68%), Gaps = 3/66 (4%)
Query: 708 TKEMTVPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTGTPDAIA 767
T+ + VP+ L+G +IGKGG+ I EIR+ +GA I+I + S +R +T+TGTP+A+
Sbjct: 1 TERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKI---PDSGSGSEERIVTITGTPEAVE 57
Query: 768 LAQYLI 773
A+ LI
Sbjct: 58 KAKELI 63
Score = 65.7 bits (161), Expect = 2e-13
Identities = 30/64 (46%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 82 LRLIVPASQCGSIIGKGGSQIKTIRETSGASVYVASDMLPNSTEREVNIKGVPDAVTQAI 141
R++VP+S G IIGKGGS IK IRE +GA + + S ER V I G P+AV +A
Sbjct: 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG-SGSEERIVTITGTPEAVEKAK 60
Query: 142 YQIC 145
I
Sbjct: 61 ELIL 64
Score = 65.7 bits (161), Expect = 2e-13
Identities = 30/64 (46%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 527 LRLIVPASQCGSIIGKGGSQIKTIRETSGASVYVASDMLPNSTEREVNIKGVPDAVTQAI 586
R++VP+S G IIGKGGS IK IRE +GA + + S ER V I G P+AV +A
Sbjct: 2 ERVLVPSSLVGRIIGKGGSTIKEIREETGAKIKIPDSG-SGSEERIVTITGTPEAVEKAK 60
Query: 587 YQIC 590
I
Sbjct: 61 ELIL 64
Score = 61.8 bits (151), Expect = 4e-12
Identities = 27/55 (49%), Positives = 39/55 (70%), Gaps = 2/55 (3%)
Query: 4 KEVGSIIGKSGETVKKLREESGSKIYI--SDSSTPERIVTVIGSMDSLFRAFSLI 56
VG IIGK G T+K++REE+G+KI I S S + ERIVT+ G+ +++ +A LI
Sbjct: 9 SLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63
Score = 61.8 bits (151), Expect = 4e-12
Identities = 27/55 (49%), Positives = 39/55 (70%), Gaps = 2/55 (3%)
Query: 449 KEVGSIIGKSGETVKKLREESGSKIYI--SDSSTPERIVTVIGSMDSLFRAFSLI 501
VG IIGK G T+K++REE+G+KI I S S + ERIVT+ G+ +++ +A LI
Sbjct: 9 SLVGRIIGKGGSTIKEIREETGAKIKIPDSGSGSEERIVTITGTPEAVEKAKELI 63
>gnl|CDD|215657 pfam00013, KH_1, KH domain. KH motifs bind RNA in vitro.
Autoantibodies to Nova, a KH domain protein, cause
paraneoplastic opsoclonus ataxia.
Length = 59
Score = 65.3 bits (160), Expect = 2e-13
Identities = 26/66 (39%), Positives = 41/66 (62%), Gaps = 7/66 (10%)
Query: 263 TKEMTVPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTGTPDAIA 322
T+ + +P + +G +IGKGG+ I EIR+ +G IRI D D T+T++GTP+ +
Sbjct: 1 TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIP-------DDRDDTVTISGTPEQVE 53
Query: 323 LAQYLI 328
A+ LI
Sbjct: 54 KAKELI 59
Score = 65.3 bits (160), Expect = 2e-13
Identities = 26/66 (39%), Positives = 41/66 (62%), Gaps = 7/66 (10%)
Query: 708 TKEMTVPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTGTPDAIA 767
T+ + +P + +G +IGKGG+ I EIR+ +G IRI D D T+T++GTP+ +
Sbjct: 1 TERILIPPDKVGRIIGKGGSNIKEIREETGVKIRIP-------DDRDDTVTISGTPEQVE 53
Query: 768 LAQYLI 773
A+ LI
Sbjct: 54 KAKELI 59
Score = 58.7 bits (143), Expect = 4e-11
Identities = 24/63 (38%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 82 LRLIVPASQCGSIIGKGGSQIKTIRETSGASVYVASDMLPNSTEREVNIKGVPDAVTQAI 141
R+++P + G IIGKGGS IK IRE +G + + P+ + V I G P+ V +A
Sbjct: 2 ERILIPPDKVGRIIGKGGSNIKEIREETGVKIRI-----PDDRDDTVTISGTPEQVEKAK 56
Query: 142 YQI 144
I
Sbjct: 57 ELI 59
Score = 58.7 bits (143), Expect = 4e-11
Identities = 24/63 (38%), Positives = 35/63 (55%), Gaps = 5/63 (7%)
Query: 527 LRLIVPASQCGSIIGKGGSQIKTIRETSGASVYVASDMLPNSTEREVNIKGVPDAVTQAI 586
R+++P + G IIGKGGS IK IRE +G + + P+ + V I G P+ V +A
Sbjct: 2 ERILIPPDKVGRIIGKGGSNIKEIREETGVKIRI-----PDDRDDTVTISGTPEQVEKAK 56
Query: 587 YQI 589
I
Sbjct: 57 ELI 59
Score = 52.2 bits (126), Expect = 7e-09
Identities = 22/53 (41%), Positives = 33/53 (62%), Gaps = 2/53 (3%)
Query: 4 KEVGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSLFRAFSLI 56
+VG IIGK G +K++REE+G KI I D + VT+ G+ + + +A LI
Sbjct: 9 DKVGRIIGKGGSNIKEIREETGVKIRIPDD--RDDTVTISGTPEQVEKAKELI 59
Score = 52.2 bits (126), Expect = 7e-09
Identities = 22/53 (41%), Positives = 33/53 (62%), Gaps = 2/53 (3%)
Query: 449 KEVGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSLFRAFSLI 501
+VG IIGK G +K++REE+G KI I D + VT+ G+ + + +A LI
Sbjct: 9 DKVGRIIGKGGSNIKEIREETGVKIRIPDD--RDDTVTISGTPEQVEKAKELI 59
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 64.6 bits (158), Expect = 4e-13
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 5/69 (7%)
Query: 260 NQITKEMTVPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTGTPD 319
+ +T E+ +P + +G +IGKGG+ I +I + +G I I S +R + +TG P+
Sbjct: 1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIP-----GPGSEERVVEITGPPE 55
Query: 320 AIALAQYLI 328
+ A LI
Sbjct: 56 NVEKAAELI 64
Score = 64.6 bits (158), Expect = 4e-13
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 5/69 (7%)
Query: 705 NQITKEMTVPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTGTPD 764
+ +T E+ +P + +G +IGKGG+ I +I + +G I I S +R + +TG P+
Sbjct: 1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIP-----GPGSEERVVEITGPPE 55
Query: 765 AIALAQYLI 773
+ A LI
Sbjct: 56 NVEKAAELI 64
Score = 59.2 bits (144), Expect = 3e-11
Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 3/69 (4%)
Query: 80 IQLRLIVPASQCGSIIGKGGSQIKTIRETSGASVYVASDMLPNSTEREVNIKGVPDAVTQ 139
+ + +++PA + G IIGKGGS IK I E +G + + P S ER V I G P+ V +
Sbjct: 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG---PGSEERVVEITGPPENVEK 59
Query: 140 AIYQICLIM 148
A I I+
Sbjct: 60 AAELILEIL 68
Score = 59.2 bits (144), Expect = 3e-11
Identities = 27/69 (39%), Positives = 39/69 (56%), Gaps = 3/69 (4%)
Query: 525 IQLRLIVPASQCGSIIGKGGSQIKTIRETSGASVYVASDMLPNSTEREVNIKGVPDAVTQ 584
+ + +++PA + G IIGKGGS IK I E +G + + P S ER V I G P+ V +
Sbjct: 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPG---PGSEERVVEITGPPENVEK 59
Query: 585 AIYQICLIM 593
A I I+
Sbjct: 60 AAELILEIL 68
Score = 58.1 bits (141), Expect = 8e-11
Identities = 23/57 (40%), Positives = 36/57 (63%)
Query: 4 KEVGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSLFRAFSLITKNI 60
+VG IIGK G T+KK+ EE+G KI I + ER+V + G +++ +A LI + +
Sbjct: 12 DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAELILEIL 68
Score = 58.1 bits (141), Expect = 8e-11
Identities = 23/57 (40%), Positives = 36/57 (63%)
Query: 449 KEVGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSLFRAFSLITKNI 505
+VG IIGK G T+KK+ EE+G KI I + ER+V + G +++ +A LI + +
Sbjct: 12 DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEERVVEITGPPENVEKAAELILEIL 68
>gnl|CDD|221895 pfam13014, KH_3, KH domain. KH motifs bind RNA in vitro. This
RNA-binding domain is required for the efficient
anchoring of ASH1-mRNA to the distal tip of the
daughter cell. ASH1 is a specific repressor of
transcription that localizes asymmetrically to the
daughter cell nucleus. RNA localisation is a widespread
mechanism for achieving localised protein synthesis.
Length = 42
Score = 47.9 bits (115), Expect = 2e-07
Identities = 23/41 (56%), Positives = 31/41 (75%), Gaps = 2/41 (4%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYISDS--STPERIVTVIG 44
VG+IIGK GET+K++REE+G+KI I + ERIVT+ G
Sbjct: 2 VGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 42
Score = 47.9 bits (115), Expect = 2e-07
Identities = 23/41 (56%), Positives = 31/41 (75%), Gaps = 2/41 (4%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYISDS--STPERIVTVIG 489
VG+IIGK GET+K++REE+G+KI I + ERIVT+ G
Sbjct: 2 VGAIIGKGGETIKEIREETGAKIQIPKPEPGSGERIVTITG 42
Score = 47.9 bits (115), Expect = 2e-07
Identities = 21/43 (48%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 90 QCGSIIGKGGSQIKTIRETSGASVYVASDMLPNSTEREVNIKG 132
G+IIGKGG IK IRE +GA + + P S ER V I G
Sbjct: 1 LVGAIIGKGGETIKEIREETGAKIQI-PKPEPGSGERIVTITG 42
Score = 47.9 bits (115), Expect = 2e-07
Identities = 21/43 (48%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 535 QCGSIIGKGGSQIKTIRETSGASVYVASDMLPNSTEREVNIKG 577
G+IIGKGG IK IRE +GA + + P S ER V I G
Sbjct: 1 LVGAIIGKGGETIKEIREETGAKIQI-PKPEPGSGERIVTITG 42
Score = 45.6 bits (109), Expect = 1e-06
Identities = 23/45 (51%), Positives = 31/45 (68%), Gaps = 3/45 (6%)
Query: 272 LIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTG 316
L+GA+IGKGG I EIR+ +GA I+I K E S +R +T+TG
Sbjct: 1 LVGAIIGKGGETIKEIREETGAKIQIPKP---EPGSGERIVTITG 42
Score = 45.6 bits (109), Expect = 1e-06
Identities = 23/45 (51%), Positives = 31/45 (68%), Gaps = 3/45 (6%)
Query: 717 LIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTG 761
L+GA+IGKGG I EIR+ +GA I+I K E S +R +T+TG
Sbjct: 1 LVGAIIGKGGETIKEIREETGAKIQIPKP---EPGSGERIVTITG 42
>gnl|CDD|239087 cd02394, vigilin_like_KH, K homology RNA-binding
domain_vigilin_like. The vigilin family is a large and
extended family of multiple KH-domain proteins,
including vigilin, also called high density lipoprotein
binding protien (HBP), fungal Scp160 and bicaudal-C.
Yeast Scp160p has been shown to bind RNA and to
associate with both soluble and membrane-bound
polyribosomes as a mRNP component. Bicaudal-C is a
RNA-binding molecule believed to function in embryonic
development at the post-transcriptional level. In
general, KH binds single-stranded RNA or DNA. It is
found in a wide variety of proteins including ribosomal
proteins, transcription factors and post-transcriptional
modifiers of mRNA.
Length = 62
Score = 47.1 bits (113), Expect = 5e-07
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 5/63 (7%)
Query: 263 TKEMTVPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTGTPDAIA 322
T+E+ +P +L +IGK G+ I +I + +G IR + + TIT+TG + +
Sbjct: 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSD-----TITITGPKENVE 55
Query: 323 LAQ 325
A+
Sbjct: 56 KAK 58
Score = 47.1 bits (113), Expect = 5e-07
Identities = 19/63 (30%), Positives = 34/63 (53%), Gaps = 5/63 (7%)
Query: 708 TKEMTVPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTGTPDAIA 767
T+E+ +P +L +IGK G+ I +I + +G IR + + TIT+TG + +
Sbjct: 1 TEEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPDPGSKSD-----TITITGPKENVE 55
Query: 768 LAQ 770
A+
Sbjct: 56 KAK 58
Score = 44.4 bits (106), Expect = 5e-06
Identities = 16/49 (32%), Positives = 27/49 (55%)
Query: 8 SIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSLFRAFSLI 56
IIGK G ++K+ EE+G KI D + +T+ G +++ +A I
Sbjct: 13 FIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEI 61
Score = 44.4 bits (106), Expect = 5e-06
Identities = 16/49 (32%), Positives = 27/49 (55%)
Query: 453 SIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSLFRAFSLI 501
IIGK G ++K+ EE+G KI D + +T+ G +++ +A I
Sbjct: 13 FIIGKKGSNIRKIMEETGVKIRFPDPGSKSDTITITGPKENVEKAKEEI 61
Score = 41.0 bits (97), Expect = 7e-05
Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 3/64 (4%)
Query: 82 LRLIVPASQCGSIIGKGGSQIKTIRETSGASVYVASDMLPNSTEREVNIKGVPDAVTQAI 141
+ +P IIGK GS I+ I E +G + P S + I G + V +A
Sbjct: 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPD---PGSKSDTITITGPKENVEKAK 58
Query: 142 YQIC 145
+I
Sbjct: 59 EEIL 62
Score = 41.0 bits (97), Expect = 7e-05
Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 3/64 (4%)
Query: 527 LRLIVPASQCGSIIGKGGSQIKTIRETSGASVYVASDMLPNSTEREVNIKGVPDAVTQAI 586
+ +P IIGK GS I+ I E +G + P S + I G + V +A
Sbjct: 2 EEVEIPKKLHRFIIGKKGSNIRKIMEETGVKIRFPD---PGSKSDTITITGPKENVEKAK 58
Query: 587 YQIC 590
+I
Sbjct: 59 EEIL 62
>gnl|CDD|237494 PRK13763, PRK13763, putative RNA-processing protein; Provisional.
Length = 180
Score = 44.1 bits (105), Expect = 8e-05
Identities = 35/135 (25%), Positives = 55/135 (40%), Gaps = 43/135 (31%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSL--FRA----------F 53
+G +IGK GET K++ E +G K+ I DS T E I+ D L +A F
Sbjct: 14 IGVLIGKKGETKKEIEERTGVKLEI-DSETGEVIIEPTDGEDPLAVLKARDIVKAIGRGF 72
Query: 54 S-------------LITKNIEEFHKNQNKHLGGNGESQLIQLRLIVPASQCGSIIGKGGS 100
S L ++ ++ + N L +++ G IIG+GG
Sbjct: 73 SPEKALRLLDDDYVLEVIDLSDYGDSPN---------ALRRIK--------GRIIGEGGK 115
Query: 101 QIKTIRETSGASVYV 115
+ I E +G + V
Sbjct: 116 TRRIIEELTGVDISV 130
Score = 44.1 bits (105), Expect = 8e-05
Identities = 35/135 (25%), Positives = 55/135 (40%), Gaps = 43/135 (31%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSMDSL--FRA----------F 498
+G +IGK GET K++ E +G K+ I DS T E I+ D L +A F
Sbjct: 14 IGVLIGKKGETKKEIEERTGVKLEI-DSETGEVIIEPTDGEDPLAVLKARDIVKAIGRGF 72
Query: 499 S-------------LITKNIEEFHKNQNKHLGGNGESQLIQLRLIVPASQCGSIIGKGGS 545
S L ++ ++ + N L +++ G IIG+GG
Sbjct: 73 SPEKALRLLDDDYVLEVIDLSDYGDSPN---------ALRRIK--------GRIIGEGGK 115
Query: 546 QIKTIRETSGASVYV 560
+ I E +G + V
Sbjct: 116 TRRIIEELTGVDISV 130
Score = 36.4 bits (85), Expect = 0.030
Identities = 15/63 (23%), Positives = 30/63 (47%), Gaps = 6/63 (9%)
Query: 261 QITKEMTVPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTGTPDA 320
+ + + +P + IG +IGK G EI + +G + I + ++ + I T D
Sbjct: 2 MMMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEI------DSETGEVIIEPTDGEDP 55
Query: 321 IAL 323
+A+
Sbjct: 56 LAV 58
Score = 36.4 bits (85), Expect = 0.030
Identities = 15/63 (23%), Positives = 30/63 (47%), Gaps = 6/63 (9%)
Query: 706 QITKEMTVPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTGTPDA 765
+ + + +P + IG +IGK G EI + +G + I + ++ + I T D
Sbjct: 2 MMMEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEI------DSETGEVIIEPTDGEDP 55
Query: 766 IAL 768
+A+
Sbjct: 56 LAV 58
>gnl|CDD|211858 TIGR03665, arCOG04150, arCOG04150 universal archaeal KH domain
protein. This family of proteins is universal among the
41 archaeal genomes analyzed in and is not observed
outside of the archaea. The proteins contain a single KH
domain (pfam00013) which is likely to confer the ability
to bind RNA.
Length = 172
Score = 41.8 bits (99), Expect = 3e-04
Identities = 42/161 (26%), Positives = 66/161 (40%), Gaps = 54/161 (33%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSM---DSLFRA---------- 52
+G +IGK GET K++ E +G K+ I DS T E V + ++ +A
Sbjct: 9 IGVLIGKGGETKKEIEERTGVKLDI-DSETGE--VKIEEEDEDPLAVMKAREVVKAIGRG 65
Query: 53 FS-------------LITKNIEEFHKNQNKHLGGNGESQLIQLRLIVPASQCGSIIGKGG 99
FS L +++E+ K+ N L +++ G IIG+GG
Sbjct: 66 FSPEKALKLLDDDYMLEVIDLKEYGKSPN---------ALRRIK--------GRIIGEGG 108
Query: 100 SQIKTIRETSGASVYVASDMLPNSTEREVNIKGVPDAVTQA 140
+ I E +G S+ V + V I G P+ V A
Sbjct: 109 KTRRIIEELTGVSISV--------YGKTVGIIGDPEQVQIA 141
Score = 41.8 bits (99), Expect = 3e-04
Identities = 42/161 (26%), Positives = 66/161 (40%), Gaps = 54/161 (33%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGSM---DSLFRA---------- 497
+G +IGK GET K++ E +G K+ I DS T E V + ++ +A
Sbjct: 9 IGVLIGKGGETKKEIEERTGVKLDI-DSETGE--VKIEEEDEDPLAVMKAREVVKAIGRG 65
Query: 498 FS-------------LITKNIEEFHKNQNKHLGGNGESQLIQLRLIVPASQCGSIIGKGG 544
FS L +++E+ K+ N L +++ G IIG+GG
Sbjct: 66 FSPEKALKLLDDDYMLEVIDLKEYGKSPN---------ALRRIK--------GRIIGEGG 108
Query: 545 SQIKTIRETSGASVYVASDMLPNSTEREVNIKGVPDAVTQA 585
+ I E +G S+ V + V I G P+ V A
Sbjct: 109 KTRRIIEELTGVSISV--------YGKTVGIIGDPEQVQIA 141
Score = 33.7 bits (78), Expect = 0.20
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 265 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTG 316
+ +P + IG +IGKGG EI + +G + I DS + +
Sbjct: 1 YVKIPKDRIGVLIGKGGETKKEIEERTGVKLDI--------DSETGEVKIEE 44
Score = 33.7 bits (78), Expect = 0.20
Identities = 14/52 (26%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 710 EMTVPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTG 761
+ +P + IG +IGKGG EI + +G + I DS + +
Sbjct: 1 YVKIPKDRIGVLIGKGGETKKEIEERTGVKLDI--------DSETGEVKIEE 44
>gnl|CDD|184311 PRK13764, PRK13764, ATPase; Provisional.
Length = 602
Score = 42.5 bits (101), Expect = 0.001
Identities = 17/49 (34%), Positives = 24/49 (48%)
Query: 267 TVPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMT 315
VP + I VIGKGG +I +I K G I + EE + + +T
Sbjct: 486 YVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEPGEEAEEGEEVT 534
Score = 42.5 bits (101), Expect = 0.001
Identities = 17/49 (34%), Positives = 24/49 (48%)
Query: 712 TVPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMT 760
VP + I VIGKGG +I +I K G I + EE + + +T
Sbjct: 486 YVPEKDIPKVIGKGGKRIKKIEKKLGIDIDVRPLDEEPGEEAEEGEEVT 534
>gnl|CDD|181413 PRK08406, PRK08406, transcription elongation factor NusA-like
protein; Validated.
Length = 140
Score = 39.8 bits (94), Expect = 0.001
Identities = 26/104 (25%), Positives = 44/104 (42%), Gaps = 20/104 (19%)
Query: 5 EVGSIIGKSGETVKKLREESGSKI-YISDSSTPERIVTVIGSMDSLFRAFSLITKNIEEF 63
++G IGK GE VK+L E+ G I + S PE + ++F ++ + I++
Sbjct: 42 DMGLAIGKGGENVKRLEEKLGKDIELVEYSDDPEEFIK------NIFAPAAVRSVTIKKK 95
Query: 64 HKNQNKHLGGNGESQLIQLRLIVPASQCGSIIGKGGSQIKTIRE 107
NG+ + V G IGK G I+ ++
Sbjct: 96 ----------NGDKVAY---VEVAPEDKGIAIGKNGKNIERAKD 126
Score = 39.8 bits (94), Expect = 0.001
Identities = 26/104 (25%), Positives = 44/104 (42%), Gaps = 20/104 (19%)
Query: 450 EVGSIIGKSGETVKKLREESGSKI-YISDSSTPERIVTVIGSMDSLFRAFSLITKNIEEF 508
++G IGK GE VK+L E+ G I + S PE + ++F ++ + I++
Sbjct: 42 DMGLAIGKGGENVKRLEEKLGKDIELVEYSDDPEEFIK------NIFAPAAVRSVTIKKK 95
Query: 509 HKNQNKHLGGNGESQLIQLRLIVPASQCGSIIGKGGSQIKTIRE 552
NG+ + V G IGK G I+ ++
Sbjct: 96 ----------NGDKVAY---VEVAPEDKGIAIGKNGKNIERAKD 126
Score = 28.3 bits (64), Expect = 9.2
Identities = 10/34 (29%), Positives = 15/34 (44%)
Query: 85 IVPASQCGSIIGKGGSQIKTIRETSGASVYVASD 118
+V G IGKGG +K + E G + +
Sbjct: 37 VVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY 70
Score = 28.3 bits (64), Expect = 9.2
Identities = 10/34 (29%), Positives = 15/34 (44%)
Query: 530 IVPASQCGSIIGKGGSQIKTIRETSGASVYVASD 563
+V G IGKGG +K + E G + +
Sbjct: 37 VVKEGDMGLAIGKGGENVKRLEEKLGKDIELVEY 70
>gnl|CDD|239086 cd02393, PNPase_KH, Polynucleotide phosphorylase (PNPase) K
homology RNA-binding domain (KH). PNPase is a
polyribonucleotide nucleotidyl transferase that
degrades mRNA in prokaryotes and plant chloroplasts.
The C-terminal region of PNPase contains domains
homologous to those in other RNA binding proteins: a KH
domain and an S1 domain. KH domains bind
single-stranded RNA and are found in a wide variety of
proteins including ribosomal proteins, transcription
factors and post-transcriptional modifiers of mRNA.
Length = 61
Score = 37.5 bits (88), Expect = 0.001
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 5/52 (9%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGS-MDSLFRAFSLI 56
+ +IG G+T+KK+ EE+G KI I D T V + S ++ +A +I
Sbjct: 13 IRDVIGPGGKTIKKIIEETGVKIDIEDDGT----VYIAASDKEAAEKAKKMI 60
Score = 37.5 bits (88), Expect = 0.001
Identities = 18/52 (34%), Positives = 29/52 (55%), Gaps = 5/52 (9%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGS-MDSLFRAFSLI 501
+ +IG G+T+KK+ EE+G KI I D T V + S ++ +A +I
Sbjct: 13 IRDVIGPGGKTIKKIIEETGVKIDIEDDGT----VYIAASDKEAAEKAKKMI 60
Score = 33.3 bits (77), Expect = 0.040
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 86 VPASQCGSIIGKGGSQIKTIRETSGASVYVASD 118
+P + +IG GG IK I E +G + + D
Sbjct: 8 IPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDD 40
Score = 33.3 bits (77), Expect = 0.040
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 531 VPASQCGSIIGKGGSQIKTIRETSGASVYVASD 563
+P + +IG GG IK I E +G + + D
Sbjct: 8 IPPDKIRDVIGPGGKTIKKIIEETGVKIDIEDD 40
Score = 32.9 bits (76), Expect = 0.057
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 266 MTVPNELIGAVIGKGGTKIFEIRKISGAMIRI 297
M +P + I VIG GG I +I + +G I I
Sbjct: 6 MKIPPDKIRDVIGPGGKTIKKIIEETGVKIDI 37
Score = 32.9 bits (76), Expect = 0.057
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 711 MTVPNELIGAVIGKGGTKIFEIRKISGAMIRI 742
M +P + I VIG GG I +I + +G I I
Sbjct: 6 MKIPPDKIRDVIGPGGKTIKKIIEETGVKIDI 37
>gnl|CDD|224019 COG1094, COG1094, Predicted RNA-binding protein (contains KH
domains) [General function prediction only].
Length = 194
Score = 40.4 bits (95), Expect = 0.002
Identities = 36/175 (20%), Positives = 59/175 (33%), Gaps = 51/175 (29%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYISDSST------PER-------------IVTVIG-- 44
+G +IGK GE K + E++G K+ I DS T R +V IG
Sbjct: 19 IGVLIGKWGEVKKAIEEKTGVKLRI-DSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRG 77
Query: 45 -SMDSLFRAFS----LITKNIEEFHKNQNKHLGGNGESQLIQLRLIVPASQCGSIIGKGG 99
+ + L ++++ HL G IIG+ G
Sbjct: 78 FPPEKALKLLEDDYYLEVIDLKDVVTLSGDHL----------------RRIKGRIIGREG 121
Query: 100 SQIKTIRETSGASVYVASDMLPNSTEREVNIKGVPDAVTQAIYQICLIMVDSPPK 154
+ I E +G + V V I G + V A + +++ +P
Sbjct: 122 KTRRAIEELTGVYISVYGK--------TVAIIGGFEQVEIAREAVEMLINGAPHG 168
Score = 40.4 bits (95), Expect = 0.002
Identities = 36/175 (20%), Positives = 59/175 (33%), Gaps = 51/175 (29%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYISDSST------PER-------------IVTVIG-- 489
+G +IGK GE K + E++G K+ I DS T R +V IG
Sbjct: 19 IGVLIGKWGEVKKAIEEKTGVKLRI-DSKTGSVTIRTTRKTEDPLALLKARDVVKAIGRG 77
Query: 490 -SMDSLFRAFS----LITKNIEEFHKNQNKHLGGNGESQLIQLRLIVPASQCGSIIGKGG 544
+ + L ++++ HL G IIG+ G
Sbjct: 78 FPPEKALKLLEDDYYLEVIDLKDVVTLSGDHL----------------RRIKGRIIGREG 121
Query: 545 SQIKTIRETSGASVYVASDMLPNSTEREVNIKGVPDAVTQAIYQICLIMVDSPPK 599
+ I E +G + V V I G + V A + +++ +P
Sbjct: 122 KTRRAIEELTGVYISVYGK--------TVAIIGGFEQVEIAREAVEMLINGAPHG 168
>gnl|CDD|224768 COG1855, COG1855, ATPase (PilT family) [General function prediction
only].
Length = 604
Score = 41.6 bits (98), Expect = 0.002
Identities = 19/38 (50%), Positives = 22/38 (57%)
Query: 268 VPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEE 305
VP + I VIGKGG +I EI K G I + EEEE
Sbjct: 492 VPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEEE 529
Score = 41.6 bits (98), Expect = 0.002
Identities = 19/38 (50%), Positives = 22/38 (57%)
Query: 713 VPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEE 750
VP + I VIGKGG +I EI K G I + EEEE
Sbjct: 492 VPEKYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEEE 529
Score = 29.6 bits (67), Expect = 9.0
Identities = 11/41 (26%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 4 KEVGSIIGKSGETVKKLREESGSKIYI--SDSSTPERIVTV 42
K + +IGK G+ +K++ ++ G KI + + V V
Sbjct: 495 KYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEEEGEKVPV 535
Score = 29.6 bits (67), Expect = 9.0
Identities = 11/41 (26%), Positives = 21/41 (51%), Gaps = 2/41 (4%)
Query: 449 KEVGSIIGKSGETVKKLREESGSKIYI--SDSSTPERIVTV 487
K + +IGK G+ +K++ ++ G KI + + V V
Sbjct: 495 KYIPKVIGKGGKRIKEIEKKLGIKIDVKPLEEEEEGEKVPV 535
>gnl|CDD|223273 COG0195, NusA, Transcription elongation factor [Transcription].
Length = 190
Score = 39.5 bits (93), Expect = 0.003
Identities = 32/136 (23%), Positives = 53/136 (38%), Gaps = 40/136 (29%)
Query: 5 EVGSIIGKSGETVKKLREESGSKI-YISDSSTPERIVTVIGSMDSLFRA--FSLITKNIE 61
VG+ IGK G VK + EE G KI + S P + ++L A S+ K +
Sbjct: 86 PVGACIGKRGSRVKAVSEELGEKIDVVEWSEDPAEFI-----KNALAPAEVLSVNIKEDD 140
Query: 62 EFHKNQNKHLGGNGESQLIQLRLIVPASQCGSIIGKGGSQIKTIRETSGASVYVASDMLP 121
G ++ +VP Q IGKGG ++ + +G
Sbjct: 141 -------------GHVAIV----VVPPDQLSLAIGKGGQNVRLASQLTG----------- 172
Query: 122 NSTEREVNIKGVPDAV 137
E++I+ + +A+
Sbjct: 173 ----WEIDIETISEAI 184
Score = 39.5 bits (93), Expect = 0.003
Identities = 32/136 (23%), Positives = 53/136 (38%), Gaps = 40/136 (29%)
Query: 450 EVGSIIGKSGETVKKLREESGSKI-YISDSSTPERIVTVIGSMDSLFRA--FSLITKNIE 506
VG+ IGK G VK + EE G KI + S P + ++L A S+ K +
Sbjct: 86 PVGACIGKRGSRVKAVSEELGEKIDVVEWSEDPAEFI-----KNALAPAEVLSVNIKEDD 140
Query: 507 EFHKNQNKHLGGNGESQLIQLRLIVPASQCGSIIGKGGSQIKTIRETSGASVYVASDMLP 566
G ++ +VP Q IGKGG ++ + +G
Sbjct: 141 -------------GHVAIV----VVPPDQLSLAIGKGGQNVRLASQLTG----------- 172
Query: 567 NSTEREVNIKGVPDAV 582
E++I+ + +A+
Sbjct: 173 ----WEIDIETISEAI 184
Score = 29.5 bits (67), Expect = 6.1
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 268 VPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEE 303
VP + + IGKGG + +++G I I SE
Sbjct: 148 VPPDQLSLAIGKGGQNVRLASQLTGWEIDIETISEA 183
Score = 29.5 bits (67), Expect = 6.1
Identities = 12/36 (33%), Positives = 18/36 (50%)
Query: 713 VPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEE 748
VP + + IGKGG + +++G I I SE
Sbjct: 148 VPPDQLSLAIGKGGQNVRLASQLTGWEIDIETISEA 183
>gnl|CDD|218305 pfam04877, Hairpins, HrpZ. HrpZ from the plant pathogen
Pseudomonas syringae binds to lipid bilayers and forms a
cation-conducting pore in vivo. This pore-forming
activity may allow nutrient release or delivery of
virulence factors during bacterial colonisation of host
plants. The family of hairpinN proteins, Harpin, has
been merged into this family. HrpN is a virulence
determinant which elicits lesion formation in
Arabidopsis and tobacco and triggers systemic resistance
in Arabidopsis.
Length = 277
Score = 38.3 bits (89), Expect = 0.011
Identities = 28/97 (28%), Positives = 37/97 (38%), Gaps = 7/97 (7%)
Query: 802 NLPSSAPLAGLNASNPLAAALPQLAQILTKPAGLNASNPLAAALPQLAQILTKPGALNAL 861
PS+A +S L + QLAQ LT ++S+PL L + G
Sbjct: 21 GRPSAATSGASTSSKELQDVIDQLAQALTGNGQGDSSSPLGKMLAKALAADPTQGKQGGY 80
Query: 862 TS-----LSAL--GGLSDLLGGGSSGGGSGNSGGFGG 891
L L L D G + GG +G S G GG
Sbjct: 81 IKGVTDALDKLIGEKLGDNFGASAGGGLNGGSSGLGG 117
>gnl|CDD|239088 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K homology
RNA-binding domain (KH). Splicing factor 1 (SF1)
specifically recognizes the intron branch point
sequence (BPS) UACUAAC in the pre-mRNA transcripts
during spliceosome assembly. We show that the KH-QUA2
region of SF1 defines an enlarged KH (hnRNP K) fold
which is necessary and sufficient for BPS binding. KH
binds single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional
modifiers of mRNA.
Length = 120
Score = 35.7 bits (83), Expect = 0.022
Identities = 13/25 (52%), Positives = 19/25 (76%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYI 30
VG I+G G T+K+L +E+G+KI I
Sbjct: 17 VGLILGPRGNTLKQLEKETGAKISI 41
Score = 35.7 bits (83), Expect = 0.022
Identities = 13/25 (52%), Positives = 19/25 (76%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYI 475
VG I+G G T+K+L +E+G+KI I
Sbjct: 17 VGLILGPRGNTLKQLEKETGAKISI 41
>gnl|CDD|234271 TIGR03591, polynuc_phos, polyribonucleotide nucleotidyltransferase.
Members of this protein family are polyribonucleotide
nucleotidyltransferase, also called polynucleotide
phosphorylase. Some members have been shown also to have
additional functions as guanosine pentaphosphate
synthetase and as poly(A) polymerase (see model
TIGR02696 for an exception clade, within this family)
[Transcription, Degradation of RNA].
Length = 684
Score = 37.5 bits (88), Expect = 0.036
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 8/60 (13%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGS-MDSLFRAFSLI---TKNIE 61
+ +IG G+ ++++ EE+G+KI I D T V + S ++ A +I T E
Sbjct: 562 IRDVIGPGGKVIREITEETGAKIDIEDDGT----VKIAASDGEAAEAAIKMIEGITAEPE 617
Score = 37.5 bits (88), Expect = 0.036
Identities = 17/60 (28%), Positives = 30/60 (50%), Gaps = 8/60 (13%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGS-MDSLFRAFSLI---TKNIE 506
+ +IG G+ ++++ EE+G+KI I D T V + S ++ A +I T E
Sbjct: 562 IRDVIGPGGKVIREITEETGAKIDIEDDGT----VKIAASDGEAAEAAIKMIEGITAEPE 617
Score = 37.5 bits (88), Expect = 0.039
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 10/65 (15%)
Query: 266 MTVPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTGT-PDAIALA 324
+ + + I VIG GG I EI + +GA I I ED D T+ + + +A A
Sbjct: 555 IKINPDKIRDVIGPGGKVIREITEETGAKIDI-------ED--DGTVKIAASDGEAAEAA 605
Query: 325 QYLIN 329
+I
Sbjct: 606 IKMIE 610
Score = 37.5 bits (88), Expect = 0.039
Identities = 20/65 (30%), Positives = 30/65 (46%), Gaps = 10/65 (15%)
Query: 711 MTVPNELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTGT-PDAIALA 769
+ + + I VIG GG I EI + +GA I I ED D T+ + + +A A
Sbjct: 555 IKINPDKIRDVIGPGGKVIREITEETGAKIDI-------ED--DGTVKIAASDGEAAEAA 605
Query: 770 QYLIN 774
+I
Sbjct: 606 IKMIE 610
Score = 32.9 bits (76), Expect = 0.83
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 86 VPASQCGSIIGKGGSQIKTIRETSGASVYVASD 118
+ + +IG GG I+ I E +GA + + D
Sbjct: 557 INPDKIRDVIGPGGKVIREITEETGAKIDIEDD 589
Score = 32.9 bits (76), Expect = 0.83
Identities = 10/33 (30%), Positives = 17/33 (51%)
Query: 531 VPASQCGSIIGKGGSQIKTIRETSGASVYVASD 563
+ + +IG GG I+ I E +GA + + D
Sbjct: 557 INPDKIRDVIGPGGKVIREITEETGAKIDIEDD 589
>gnl|CDD|224106 COG1185, Pnp, Polyribonucleotide nucleotidyltransferase
(polynucleotide phosphorylase) [Translation, ribosomal
structure and biogenesis].
Length = 692
Score = 36.8 bits (86), Expect = 0.054
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 4/40 (10%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGS 45
+ +IG G+T+K + EE+G KI I D T V + S
Sbjct: 563 IRDVIGPGGKTIKAITEETGVKIDIEDDGT----VKIAAS 598
Score = 36.8 bits (86), Expect = 0.054
Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 4/40 (10%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGS 490
+ +IG G+T+K + EE+G KI I D T V + S
Sbjct: 563 IRDVIGPGGKTIKAITEETGVKIDIEDDGT----VKIAAS 598
Score = 34.1 bits (79), Expect = 0.44
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 266 MTVPNELIGAVIGKGGTKIFEIRKISGAMIRI 297
+ + + I VIG GG I I + +G I I
Sbjct: 556 IKIDPDKIRDVIGPGGKTIKAITEETGVKIDI 587
Score = 34.1 bits (79), Expect = 0.44
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 711 MTVPNELIGAVIGKGGTKIFEIRKISGAMIRI 742
+ + + I VIG GG I I + +G I I
Sbjct: 556 IKIDPDKIRDVIGPGGKTIKAITEETGVKIDI 587
Score = 33.7 bits (78), Expect = 0.49
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 86 VPASQCGSIIGKGGSQIKTIRETSGASVYVASD 118
+ + +IG GG IK I E +G + + D
Sbjct: 558 IDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD 590
Score = 33.7 bits (78), Expect = 0.49
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 531 VPASQCGSIIGKGGSQIKTIRETSGASVYVASD 563
+ + +IG GG IK I E +G + + D
Sbjct: 558 IDPDKIRDVIGPGGKTIKAITEETGVKIDIEDD 590
>gnl|CDD|236995 PRK11824, PRK11824, polynucleotide phosphorylase/polyadenylase;
Provisional.
Length = 693
Score = 37.0 bits (87), Expect = 0.056
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 4/40 (10%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGS 45
+ +IG G+T++++ EE+G+KI I D T V + +
Sbjct: 565 IRDVIGPGGKTIREITEETGAKIDIEDDGT----VKIAAT 600
Score = 37.0 bits (87), Expect = 0.056
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 4/40 (10%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYISDSSTPERIVTVIGS 490
+ +IG G+T++++ EE+G+KI I D T V + +
Sbjct: 565 IRDVIGPGGKTIREITEETGAKIDIEDDGT----VKIAAT 600
Score = 35.8 bits (84), Expect = 0.13
Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 16/68 (23%)
Query: 266 MTVPNELIGAVIGKGGTKIFEIRKI---SGAMIRISKSSEEEEDSNDRTITMTGT-PDAI 321
+ +P + I VIG GG K IR+I +GA I I ED D T+ + T +A
Sbjct: 558 IKIPPDKIRDVIGPGG-KT--IREITEETGAKIDI-------ED--DGTVKIAATDGEAA 605
Query: 322 ALAQYLIN 329
A+ I
Sbjct: 606 EAAKERIE 613
Score = 35.8 bits (84), Expect = 0.13
Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 16/68 (23%)
Query: 711 MTVPNELIGAVIGKGGTKIFEIRKI---SGAMIRISKSSEEEEDSNDRTITMTGT-PDAI 766
+ +P + I VIG GG K IR+I +GA I I ED D T+ + T +A
Sbjct: 558 IKIPPDKIRDVIGPGG-KT--IREITEETGAKIDI-------ED--DGTVKIAATDGEAA 605
Query: 767 ALAQYLIN 774
A+ I
Sbjct: 606 EAAKERIE 613
Score = 31.9 bits (74), Expect = 1.7
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 8/34 (23%)
Query: 92 GSIIGKGGSQIKTIRETSGAS--------VYVAS 117
+IG GG I+ I E +GA V +A+
Sbjct: 566 RDVIGPGGKTIREITEETGAKIDIEDDGTVKIAA 599
Score = 31.9 bits (74), Expect = 1.7
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 8/34 (23%)
Query: 537 GSIIGKGGSQIKTIRETSGAS--------VYVAS 562
+IG GG I+ I E +GA V +A+
Sbjct: 566 RDVIGPGGKTIREITEETGAKIDIEDDGTVKIAA 599
>gnl|CDD|203707 pfam07650, KH_2, KH domain.
Length = 77
Score = 32.9 bits (76), Expect = 0.072
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 81 QLRLIVPASQCGSIIGKGGSQIKTIRETSG 110
++ +++ SQ G +IGKGGS IK + +
Sbjct: 26 RVIVVIRTSQPGIVIGKGGSNIKKLGKELR 55
Score = 32.9 bits (76), Expect = 0.072
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 526 QLRLIVPASQCGSIIGKGGSQIKTIRETSG 555
++ +++ SQ G +IGKGGS IK + +
Sbjct: 26 RVIVVIRTSQPGIVIGKGGSNIKKLGKELR 55
Score = 30.6 bits (70), Expect = 0.50
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 7 GSIIGKSGETVKKLREESGSKIYISDS 33
G +IGK G +KKL +E I +
Sbjct: 37 GIVIGKGGSNIKKLGKELRKLIELEGK 63
Score = 30.6 bits (70), Expect = 0.50
Identities = 10/27 (37%), Positives = 14/27 (51%)
Query: 452 GSIIGKSGETVKKLREESGSKIYISDS 478
G +IGK G +KKL +E I +
Sbjct: 37 GIVIGKGGSNIKKLGKELRKLIELEGK 63
Score = 28.3 bits (64), Expect = 3.4
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 274 GAVIGKGGTKIFEIRKISGAMIRISKS 300
G VIGKGG+ I ++ K +I +
Sbjct: 37 GIVIGKGGSNIKKLGKELRKLIELEGK 63
Score = 28.3 bits (64), Expect = 3.4
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 719 GAVIGKGGTKIFEIRKISGAMIRISKS 745
G VIGKGG+ I ++ K +I +
Sbjct: 37 GIVIGKGGSNIKKLGKELRKLIELEGK 63
>gnl|CDD|233653 TIGR01952, nusA_arch, NusA family KH domain protein, archaeal.
This model represents a family of archaeal proteins
found in a single copy per genome. It contains two KH
domains (pfam00013) and is most closely related to the
central region bacterial NusA, a transcription
termination factor named for its iteraction with phage
lambda protein N in E. coli. The proteins required for
antitermination by N include NusA, NusB, nusE (ribosomal
protein S10), and nusG. This system, on the whole,
appears not to be present in the Archaea.
Length = 141
Score = 34.3 bits (79), Expect = 0.10
Identities = 28/104 (26%), Positives = 41/104 (39%), Gaps = 20/104 (19%)
Query: 5 EVGSIIGKSGETVKKLREESGSKI-YISDSSTPERIVTVIGSMDSLFRAFSLITKNIEEF 63
E+G+ IGK GE VK+L E G I I S E F A L ++
Sbjct: 43 EMGAAIGKGGENVKRLEELIGKSIELIEYSENLE-----------EFVANKLAPAEVKNV 91
Query: 64 HKNQNKHLGGNGESQLIQLRLIVPASQCGSIIGKGGSQIKTIRE 107
++ + + + P + G IGKGG I+ +E
Sbjct: 92 TVSEF-------NGKKVAYVEVHPRDK-GIAIGKGGKNIERAKE 127
Score = 34.3 bits (79), Expect = 0.10
Identities = 28/104 (26%), Positives = 41/104 (39%), Gaps = 20/104 (19%)
Query: 450 EVGSIIGKSGETVKKLREESGSKI-YISDSSTPERIVTVIGSMDSLFRAFSLITKNIEEF 508
E+G+ IGK GE VK+L E G I I S E F A L ++
Sbjct: 43 EMGAAIGKGGENVKRLEELIGKSIELIEYSENLE-----------EFVANKLAPAEVKNV 91
Query: 509 HKNQNKHLGGNGESQLIQLRLIVPASQCGSIIGKGGSQIKTIRE 552
++ + + + P + G IGKGG I+ +E
Sbjct: 92 TVSEF-------NGKKVAYVEVHPRDK-GIAIGKGGKNIERAKE 127
>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex
non-fungal. The approx. 70 residue Med15 domain of the
ARC-Mediator co-activator is a three-helix bundle with
marked similarity to the KIX domain. The sterol
regulatory element binding protein (SREBP) family of
transcription activators use the ARC105 subunit to
activate target genes in the regulation of cholesterol
and fatty acid homeostasis. In addition, Med15 is a
critical transducer of gene activation signals that
control early metazoan development.
Length = 768
Score = 35.7 bits (82), Expect = 0.13
Identities = 31/110 (28%), Positives = 43/110 (39%), Gaps = 17/110 (15%)
Query: 159 PYRPLPQNAGGPGLIGNQFGMQNSL-------MGAPDMGNNPLAGLAALGLGGNSGGGMG 211
P RP+ Q GGPG N + SL MGA MG + ++ + + GG +GG M
Sbjct: 96 PGRPMGQQMGGPGTASN---LLQSLNVRGQMPMGAAGMGPHQMSRVGTMQPGGQAGGMMQ 152
Query: 212 GGLNAAALAALASSQLKTNHMPRNQNQNQNQHNRNNRDGPSQKTNQQQNQ 261
++ + N M Q Q Q Q N+ QQ Q
Sbjct: 153 Q-------SSGQPQSQQPNQMGPQQGQAQGQAGGMNQGQQGPVGQQQPPQ 195
Score = 35.7 bits (82), Expect = 0.13
Identities = 31/110 (28%), Positives = 43/110 (39%), Gaps = 17/110 (15%)
Query: 604 PYRPLPQNAGGPGLIGNQFGMQNSL-------MGAPDMGNNPLAGLAALGLGGNSGGGMG 656
P RP+ Q GGPG N + SL MGA MG + ++ + + GG +GG M
Sbjct: 96 PGRPMGQQMGGPGTASN---LLQSLNVRGQMPMGAAGMGPHQMSRVGTMQPGGQAGGMMQ 152
Query: 657 GGLNAAALAALASSQLKTNHMPRNQNQNQNQHNRNNRDGPSQKTNQQQNQ 706
++ + N M Q Q Q Q N+ QQ Q
Sbjct: 153 Q-------SSGQPQSQQPNQMGPQQGQAQGQAGGMNQGQQGPVGQQQPPQ 195
>gnl|CDD|236382 PRK09111, PRK09111, DNA polymerase III subunits gamma and tau;
Validated.
Length = 598
Score = 34.1 bits (79), Expect = 0.34
Identities = 29/100 (29%), Positives = 33/100 (33%), Gaps = 14/100 (14%)
Query: 818 LAAAL--PQLA---QILTKPAGL----NASNPLAAA---LPQLAQILTKPGALNALTSLS 865
A L L+ Q+L K G+ A PLAAA L +LA P AL L
Sbjct: 331 FAKKLSMRVLSRLWQMLLK--GIEEVQGAPRPLAAAEMVLIRLAYAADLPTPDEALRRLQ 388
Query: 866 ALGGLSDLLGGGSSGGGSGNSGGFGGVPQGPNYANIQTTG 905
GGG GGG G A G
Sbjct: 389 EGPPSPGGGGGGPPGGGGAPGAPAAAAAPGAAAAAPAAGG 428
Score = 30.3 bits (69), Expect = 6.5
Identities = 22/73 (30%), Positives = 23/73 (31%), Gaps = 3/73 (4%)
Query: 368 NASNPLAAA---LPQLAQILTKPGALNALTSLSALGGLSDLLGGGSSGGGSGNSGGFGGV 424
A PLAAA L +LA P AL L GGG GGG
Sbjct: 356 GAPRPLAAAEMVLIRLAYAADLPTPDEALRRLQEGPPSPGGGGGGPPGGGGAPGAPAAAA 415
Query: 425 PQGPNYANIQTTG 437
G A G
Sbjct: 416 APGAAAAAPAAGG 428
>gnl|CDD|218059 pfam04391, DUF533, Protein of unknown function (DUF533). Some
family members may be secreted or integral membrane
proteins.
Length = 187
Score = 32.9 bits (76), Expect = 0.45
Identities = 28/120 (23%), Positives = 41/120 (34%), Gaps = 10/120 (8%)
Query: 189 MGNNPLAGLAALGLGGNSGGGMGGG-LNAAALAALASSQLKTNHMPRNQNQNQNQHNRNN 247
G L GL LGG G MGG L LAAL + Q+ Q+
Sbjct: 6 GGGGGLGGLLGALLGGKKGRKMGGKALKYGGLAALGG-------LAYKAYQDWQQNQGTA 58
Query: 248 RDGPSQKTNQQQNQITKEMTVP--NELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEE 305
G Q +Q ++ ++ +I A G E +I + + +EE
Sbjct: 59 AAGEPQPLDQLPPADEEQHSLLLLRAMIAAAKADGHIDEEERARIEQELGELGLDAEERA 118
Score = 32.9 bits (76), Expect = 0.45
Identities = 28/120 (23%), Positives = 41/120 (34%), Gaps = 10/120 (8%)
Query: 634 MGNNPLAGLAALGLGGNSGGGMGGG-LNAAALAALASSQLKTNHMPRNQNQNQNQHNRNN 692
G L GL LGG G MGG L LAAL + Q+ Q+
Sbjct: 6 GGGGGLGGLLGALLGGKKGRKMGGKALKYGGLAALGG-------LAYKAYQDWQQNQGTA 58
Query: 693 RDGPSQKTNQQQNQITKEMTVP--NELIGAVIGKGGTKIFEIRKISGAMIRISKSSEEEE 750
G Q +Q ++ ++ +I A G E +I + + +EE
Sbjct: 59 AAGEPQPLDQLPPADEEQHSLLLLRAMIAAAKADGHIDEEERARIEQELGELGLDAEERA 118
>gnl|CDD|224081 COG1159, Era, GTPase [General function prediction only].
Length = 298
Score = 32.9 bits (76), Expect = 0.69
Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 56 ITKNIEEFHKNQNKHLGGNGESQLIQLRLIVP-ASQCGSIIGKGGSQIKTI 105
+ IEEF + + L I + V SQ G IIGK G+ IK I
Sbjct: 212 VAVEIEEFEEREKGLL-------KIHATIYVERESQKGIIIGKNGAMIKKI 255
Score = 32.9 bits (76), Expect = 0.69
Identities = 18/51 (35%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 501 ITKNIEEFHKNQNKHLGGNGESQLIQLRLIVP-ASQCGSIIGKGGSQIKTI 550
+ IEEF + + L I + V SQ G IIGK G+ IK I
Sbjct: 212 VAVEIEEFEEREKGLL-------KIHATIYVERESQKGIIIGKNGAMIKKI 255
>gnl|CDD|239049 cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH). NusA is
an essential multifunctional transcription elongation
factor that is universally conserved among prokaryotes
and archaea. NusA anti-termination function plays an
important role in the expression of ribosomal rrn
operons. During transcription of many other genes,
NusA-induced RNAP pausing provides a mechanism for
synchronizing transcription and translation . The
N-terminal RNAP-binding domain (NTD) is connected
through a flexible hinge helix to three globular
domains, S1, KH1 and KH2. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices.
Length = 61
Score = 29.8 bits (68), Expect = 0.71
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 83 RLIVPASQCGSIIGKGGSQIKTIRETSG 110
R++VP Q G IGKGG ++ + G
Sbjct: 28 RVVVPDDQLGLAIGKGGQNVRLASKLLG 55
Score = 29.8 bits (68), Expect = 0.71
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 528 RLIVPASQCGSIIGKGGSQIKTIRETSG 555
R++VP Q G IGKGG ++ + G
Sbjct: 28 RVVVPDDQLGLAIGKGGQNVRLASKLLG 55
Score = 28.3 bits (64), Expect = 2.2
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 4 KEVGSIIGKSGETVKKLREESGSKI 28
++G IGK G+ V+ + G KI
Sbjct: 34 DQLGLAIGKGGQNVRLASKLLGEKI 58
Score = 28.3 bits (64), Expect = 2.2
Identities = 9/25 (36%), Positives = 14/25 (56%)
Query: 449 KEVGSIIGKSGETVKKLREESGSKI 473
++G IGK G+ V+ + G KI
Sbjct: 34 DQLGLAIGKGGQNVRLASKLLGEKI 58
>gnl|CDD|227503 COG5176, MSL5, Splicing factor (branch point binding protein) [RNA
processing and modification].
Length = 269
Score = 32.6 bits (74), Expect = 0.74
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 6 VGSIIGKSGETVKKLREESGSKIYI 30
VG +IG G T+K+L S +KI I
Sbjct: 165 VGLLIGPRGSTLKQLERISRAKIAI 189
Score = 32.6 bits (74), Expect = 0.74
Identities = 12/25 (48%), Positives = 16/25 (64%)
Query: 451 VGSIIGKSGETVKKLREESGSKIYI 475
VG +IG G T+K+L S +KI I
Sbjct: 165 VGLLIGPRGSTLKQLERISRAKIAI 189
>gnl|CDD|224750 COG1837, COG1837, Predicted RNA-binding protein (contains KH
domain) [General function prediction only].
Length = 76
Score = 29.8 bits (68), Expect = 1.1
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 78 QLIQLRLIVPASQCGSIIGKGGSQIKTIR 106
+ + + L V G +IGK G I+ IR
Sbjct: 28 KTVTIELRVAPEDMGKVIGKQGRTIQAIR 56
Score = 29.8 bits (68), Expect = 1.1
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 523 QLIQLRLIVPASQCGSIIGKGGSQIKTIR 551
+ + + L V G +IGK G I+ IR
Sbjct: 28 KTVTIELRVAPEDMGKVIGKQGRTIQAIR 56
>gnl|CDD|215598 PLN03138, PLN03138, Protein TOC75; Provisional.
Length = 796
Score = 32.5 bits (74), Expect = 1.2
Identities = 25/105 (23%), Positives = 35/105 (33%), Gaps = 2/105 (1%)
Query: 788 GGGESNMDDFSSDNNLPSSAPLAGLNASNPLA-AALPQLAQILTKPAGLNASNPLAAALP 846
G S M ++ +L SS P +S A A + A +AS+ ++
Sbjct: 1 GRSSSTMVSAAASTSLSSSRPQLSSFSSRSPQSATRSPRASSIKCSASASASSSATSSSA 60
Query: 847 QLAQILTKPGALNALTSLSALGGLSDLLGGGSSGGGSGNSGGFGG 891
L + GG GG GGG G GG G
Sbjct: 61 SLVANGAVALLSAS-AISGGGGGGGGGFGGFGGGGGGGGGGGGGW 104
>gnl|CDD|235233 PRK04163, PRK04163, exosome complex RNA-binding protein Rrp4;
Provisional.
Length = 235
Score = 31.8 bits (73), Expect = 1.3
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 94 IIGKGGSQIKTIRETSGASVYVA 116
+IGK GS I ++E +G + V
Sbjct: 159 VIGKKGSMINMLKEETGCDIIVG 181
Score = 31.8 bits (73), Expect = 1.3
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 539 IIGKGGSQIKTIRETSGASVYVA 561
+IGK GS I ++E +G + V
Sbjct: 159 VIGKKGSMINMLKEETGCDIIVG 181
>gnl|CDD|179216 PRK01064, PRK01064, hypothetical protein; Provisional.
Length = 78
Score = 28.4 bits (63), Expect = 3.5
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 54 SLITKNIEEFHKNQNKHLGGNGESQLIQLRLIVPASQCGSIIGKGGSQIKTIR 106
+ I KN+ + + + H+ + I L V G IIGK G IK IR
Sbjct: 6 AYIVKNLVD--RPEEVHIKEVQGTHTIIYELTVAKPDIGKIIGKEGRTIKAIR 56
Score = 28.4 bits (63), Expect = 3.5
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 499 SLITKNIEEFHKNQNKHLGGNGESQLIQLRLIVPASQCGSIIGKGGSQIKTIR 551
+ I KN+ + + + H+ + I L V G IIGK G IK IR
Sbjct: 6 AYIVKNLVD--RPEEVHIKEVQGTHTIIYELTVAKPDIGKIIGKEGRTIKAIR 56
>gnl|CDD|176214 cd08252, AL_MDR, Arginate lyase and other MDR family members. This
group contains a structure identified as an arginate
lyase. Other members are identified quinone reductases,
alginate lyases, and other proteins related to the
zinc-dependent dehydrogenases/reductases. QOR catalyzes
the conversion of a quinone and NAD(P)H to a
hydroquinone and NAD(P+. Quinones are cyclic diones
derived from aromatic compounds. Membrane bound QOR acts
in the respiratory chains of bacteria and mitochondria,
while soluble QOR acts to protect from toxic quinones
(e.g. DT-diaphorase) or as a soluble eye-lens protein in
some vertebrates (e.g. zeta-crystalin). QOR reduces
quinones through a semi-quinone intermediate via a
NAD(P)H-dependent single electron transfer. QOR is a
member of the medium chain dehydrogenase/reductase
family, but lacks the zinc-binding sites of the
prototypical alcohol dehydrogenases of this group.
Alcohol dehydrogenase in the liver converts ethanol and
NAD+ to acetaldehyde and NADH, while in yeast and some
other microorganisms ADH catalyzes the conversion
acetaldehyde to ethanol in alcoholic fermentation. ADH
is a member of the medium chain alcohol dehydrogenase
family (MDR), which has a NAD(P)(H)-binding domain in a
Rossmann fold of a beta-alpha form. The NAD(H)-binding
region is comprised of 2 structurally similar halves,
each of which contacts a mononucleotide. The N-terminal
catalytic domain has a distant homology to GroES. These
proteins typically form dimers (typically higher plants,
mammals) or tetramers (yeast, bacteria), and have 2
tightly bound zinc atoms per subunit, a catalytic zinc
at the active site and a structural zinc in a lobe of
the catalytic domain. NAD(H) binding occurs in the cleft
between the catalytic and coenzyme-binding domains at
the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
In human ADH catalysis, the zinc ion helps coordinate
the alcohol, followed by deprotonation of a histidine,
the ribose of NAD, a serine, then the alcohol, which
allows the transfer of a hydride to NAD+, creating NADH
and a zinc-bound aldehyde or ketone. In yeast and some
bacteria, the active site zinc binds an aldehyde,
polarizing it, and leading to the reverse reaction.
Length = 336
Score = 30.6 bits (70), Expect = 4.0
Identities = 24/67 (35%), Positives = 26/67 (38%), Gaps = 20/67 (29%)
Query: 831 KPAGLNASNPLAAALPQLAQILTKPGALNALTSLSALGGLSDLLGGGSSGGGSGNS---- 886
KP L S AAALP LTSL+A L D LG G +
Sbjct: 113 KPKSL--SFAEAAALP--------------LTSLTAWEALFDRLGISEDAENEGKTLLII 156
Query: 887 GGFGGVP 893
GG GGV
Sbjct: 157 GGAGGVG 163
Score = 29.4 bits (67), Expect = 9.3
Identities = 20/56 (35%), Positives = 22/56 (39%), Gaps = 18/56 (32%)
Query: 374 AAALPQLAQILTKPGALNALTSLSALGGLSDLLGGGSSGGGSGNS----GGFGGVP 425
AAALP LTSL+A L D LG G + GG GGV
Sbjct: 122 AAALP--------------LTSLTAWEALFDRLGISEDAENEGKTLLIIGGAGGVG 163
>gnl|CDD|239095 cd02412, 30S_S3_KH, K homology RNA-binding (KH) domain of the
prokaryotic 30S small ribosomal subunit protein S3. S3
is part of the head region of the 30S ribosomal subunit
and is believed to interact with mRNA as it threads its
way from the latch into the channel. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In general, KH
binds single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional
modifiers of mRNA.
Length = 109
Score = 29.0 bits (66), Expect = 4.4
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 7 GSIIGKSGETVKKLREE 23
G IIGK G ++KLR+E
Sbjct: 73 GIIIGKKGAGIEKLRKE 89
Score = 29.0 bits (66), Expect = 4.4
Identities = 10/17 (58%), Positives = 13/17 (76%)
Query: 452 GSIIGKSGETVKKLREE 468
G IIGK G ++KLR+E
Sbjct: 73 GIIIGKKGAGIEKLRKE 89
>gnl|CDD|180801 PRK07033, PRK07033, hypothetical protein; Provisional.
Length = 427
Score = 30.4 bits (69), Expect = 5.2
Identities = 18/69 (26%), Positives = 28/69 (40%), Gaps = 5/69 (7%)
Query: 792 SNMDDFSSDNNLPSSAPLAGLN-ASNPLAAALPQLAQILTKPAGLN----ASNPLAAALP 846
++ D FS+ + A+ P A A Q +GLN A+NPL +P
Sbjct: 2 TSSDPFSAGSGGFVPPNPGDRTPAAAPAAGAPFQPRPGRGAASGLNPLVAAANPLLNLIP 61
Query: 847 QLAQILTKP 855
Q+ + P
Sbjct: 62 QIRSTVHHP 70
>gnl|CDD|234624 PRK00089, era, GTPase Era; Reviewed.
Length = 292
Score = 30.0 bits (69), Expect = 5.7
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 89 SQCGSIIGKGGSQIKTI 105
SQ G IIGKGG+ +K I
Sbjct: 236 SQKGIIIGKGGAMLKKI 252
Score = 30.0 bits (69), Expect = 5.7
Identities = 11/17 (64%), Positives = 13/17 (76%)
Query: 534 SQCGSIIGKGGSQIKTI 550
SQ G IIGKGG+ +K I
Sbjct: 236 SQKGIIIGKGGAMLKKI 252
>gnl|CDD|234722 PRK00310, rpsC, 30S ribosomal protein S3; Reviewed.
Length = 232
Score = 29.7 bits (68), Expect = 6.0
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 7 GSIIGKSGETVKKLREE 23
G +IGK G ++KLR+E
Sbjct: 74 GIVIGKKGAEIEKLRKE 90
Score = 29.7 bits (68), Expect = 6.0
Identities = 9/17 (52%), Positives = 13/17 (76%)
Query: 452 GSIIGKSGETVKKLREE 468
G +IGK G ++KLR+E
Sbjct: 74 GIVIGKKGAEIEKLRKE 90
Score = 29.0 bits (66), Expect = 9.8
Identities = 8/27 (29%), Positives = 20/27 (74%)
Query: 81 QLRLIVPASQCGSIIGKGGSQIKTIRE 107
++R+ + ++ G +IGK G++I+ +R+
Sbjct: 63 RVRVTIHTARPGIVIGKKGAEIEKLRK 89
Score = 29.0 bits (66), Expect = 9.8
Identities = 8/27 (29%), Positives = 20/27 (74%)
Query: 526 QLRLIVPASQCGSIIGKGGSQIKTIRE 552
++R+ + ++ G +IGK G++I+ +R+
Sbjct: 63 RVRVTIHTARPGIVIGKKGAEIEKLRK 89
>gnl|CDD|176204 cd08242, MDR_like, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group contains members identified as related to
zinc-dependent alcohol dehydrogenase and other members
of the MDR family, including threonine dehydrogenase.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group includes
various activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has a
catalytic role, while structural zinc aids in stability.
ADH-like proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and generally have 2 tightly bound zinc atoms per
subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 319
Score = 29.9 bits (68), Expect = 6.1
Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 276 VIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTGTPDAIALAQYLI 328
++G+ K+ + + G + +E E D + TG+P + LA L+
Sbjct: 184 LVGRHSEKL-ALARRLGVETVLPDEAESEGGGFDVVVEATGSPSGLELALRLV 235
Score = 29.9 bits (68), Expect = 6.1
Identities = 12/53 (22%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 721 VIGKGGTKIFEIRKISGAMIRISKSSEEEEDSNDRTITMTGTPDAIALAQYLI 773
++G+ K+ + + G + +E E D + TG+P + LA L+
Sbjct: 184 LVGRHSEKL-ALARRLGVETVLPDEAESEGGGFDVVVEATGSPSGLELALRLV 235
>gnl|CDD|236951 PRK11667, PRK11667, hypothetical protein; Provisional.
Length = 163
Score = 29.3 bits (66), Expect = 6.1
Identities = 14/67 (20%), Positives = 27/67 (40%), Gaps = 1/67 (1%)
Query: 360 SSAPLAGLNASNPLAAALPQLAQILTKPGALNALTSLSALGGLSDLLGGGSSGGGSGNSG 419
++A ++ + L +L A L ++ +L L+ LL GG +G+
Sbjct: 15 AAALISTGAHAASLGDSLSSAASQLGGQAG-SSQQGGWSLSSLTGLLSGGGQALSAGSMN 73
Query: 420 GFGGVPQ 426
G+ Q
Sbjct: 74 NAAGILQ 80
>gnl|CDD|218221 pfam04709, AMH_N, Anti-Mullerian hormone, N terminal region.
Anti-Mullerian hormone, AMH is a signalling molecule
involved in male and female sexual differentiation.
Defects in synthesis or action of AMH cause persistent
Mullerian duct syndrome (PMDS), a rare form of male
pseudohermaphroditism. This family represents the N
terminal part of the protein, which is not thought to be
essential for activity. AMH contains a TGF-beta domain
(pfam00019), at the C terminus.
Length = 373
Score = 29.3 bits (66), Expect = 9.1
Identities = 23/99 (23%), Positives = 27/99 (27%), Gaps = 11/99 (11%)
Query: 802 NLPSS-APLAGL-NASNPLAAALPQLAQILTKPAG-LNASNPLA--------AALPQLAQ 850
L SS L L N+ P P L G S L AA +L
Sbjct: 255 GLSSSETLLERLLNSEEPTLFLFPGWGAGLQGHRGEWALSPALLEVLRQRLQAAAAELRD 314
Query: 851 ILTKPGALNALTSLSALGGLSDLLGGGSSGGGSGNSGGF 889
P A + L L L L + GG
Sbjct: 315 EPVGPPATDLLQRLLELCALPPEGEDSPAAGGPPGEAQL 353
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 0.130 0.361
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 46,041,894
Number of extensions: 4642521
Number of successful extensions: 5425
Number of sequences better than 10.0: 1
Number of HSP's gapped: 5291
Number of HSP's successfully gapped: 185
Length of query: 914
Length of database: 10,937,602
Length adjustment: 106
Effective length of query: 808
Effective length of database: 6,236,078
Effective search space: 5038751024
Effective search space used: 5038751024
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: 64 (28.4 bits)