RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4735
(1232 letters)
>gnl|CDD|238192 cd00315, Cyt_C5_DNA_methylase, Cytosine-C5 specific DNA methylases;
Methyl transfer reactions play an important role in many
aspects of biology. Cytosine-specific DNA methylases are
found both in prokaryotes and eukaryotes. DNA
methylation, or the covalent addition of a methyl group
to cytosine within the context of the CpG dinucleotide,
has profound effects on the mammalian genome. These
effects include transcriptional repression via
inhibition of transcription factor binding or the
recruitment of methyl-binding proteins and their
associated chromatin remodeling factors, X chromosome
inactivation, imprinting and the suppression of
parasitic DNA sequences. DNA methylation is also
essential for proper embryonic development and is an
important player in both DNA repair and genome
stability.
Length = 275
Score = 64.9 bits (159), Expect = 3e-11
Identities = 24/83 (28%), Positives = 36/83 (43%), Gaps = 8/83 (9%)
Query: 561 EEIAPNATGAYQNQENSVNTLLANQNEATLLQELKRLNLRYFSPDEIRKLMCFPDECQFP 620
+E +P T +Y SV+ K N+R +P E +L FPD+ +FP
Sbjct: 194 DEPSPTLTASYGKGTGSVH-------PTAPDMIGKESNIRRLTPRECARLQGFPDDFEFP 246
Query: 621 PDCSDKARYKLLGNSINVHVVAY 643
S Y+ +GNS+ V V
Sbjct: 247 GK-SVTQAYRQIGNSVPVPVAEA 268
Score = 62.3 bits (152), Expect = 3e-10
Identities = 26/119 (21%), Positives = 40/119 (33%), Gaps = 10/119 (8%)
Query: 1101 IARTNEREAKREDISPNVTGANQRDGSVNALGTNENAGNSVTTTRTNQNEESSVNTLETN 1160
I + P + + + L + S T T + SV+
Sbjct: 160 IGIRKDLILNFFSPFPKPSEKKKTLK--DILRIRDPDEPSPTLTASYGKGTGSVH----- 212
Query: 1161 QNEATLLQELKRLNLRYFSPDEIRKLMCFPDECRFPPDCSDKSRYKLLGNSINVHVVAY 1219
K N+R +P E +L FPD+ FP S Y+ +GNS+ V V
Sbjct: 213 --PTAPDMIGKESNIRRLTPRECARLQGFPDDFEFPGK-SVTQAYRQIGNSVPVPVAEA 268
Score = 61.5 bits (150), Expect = 6e-10
Identities = 19/58 (32%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 823 NEATLLQELKRLNLRYFSPDEIRKLMCFPDDCRFPPDCSDKSRYKLLGNSINVHVVAY 880
+ K N+R +P E +L FPDD FP S Y+ +GNS+ V V
Sbjct: 212 HPTAPDMIGKESNIRRLTPRECARLQGFPDDFEFPGK-SVTQAYRQIGNSVPVPVAEA 268
Score = 46.1 bits (110), Expect = 6e-05
Identities = 11/37 (29%), Positives = 19/37 (51%)
Query: 297 SMLTRAGFRFQEFLLSPTQFGVPNSRTRYYLIAKRSP 333
+ L G+ LL+ + +GVP +R R ++I R
Sbjct: 129 NTLEELGYNVYWKLLNASDYGVPQNRERVFIIGIRKD 165
>gnl|CDD|215747 pfam00145, DNA_methylase, C-5 cytosine-specific DNA methylase.
Length = 320
Score = 43.8 bits (104), Expect = 4e-04
Identities = 25/154 (16%), Positives = 46/154 (29%), Gaps = 15/154 (9%)
Query: 500 KKILDERVKDAQNRVDLEKNPEETVNDASNSNVITTNITEINQNETKSKHIARTNESEAK 559
+ L + +T+ D + N ++ H R ++A
Sbjct: 161 RNDLILNFPVPEFDFPKPSTATDTIRDLLEEPSLDENKYNLSDKFV-ENHERRKPTTKAP 219
Query: 560 REEIAPNATGAYQNQENSVNTLLAN--------QNEATLLQELKRL----NLRYFSPDEI 607
++ + +L + N+R +P E
Sbjct: 220 GGGYPTYLLRNRIDKVEEGKGPSFTYRKSGRGEAPKTGILGKNGERFRPKNIRRLTPREC 279
Query: 608 RKLMCFPDECQFPPDCSDKARYKLLGNSINVHVV 641
+L FPD+ FP S YK +GN++ V V
Sbjct: 280 ARLQGFPDDFIFPG--SKTQLYKQIGNAVPVPVA 311
Score = 41.5 bits (98), Expect = 0.002
Identities = 18/44 (40%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 835 NLRYFSPDEIRKLMCFPDDCRFPPDCSDKSRYKLLGNSINVHVV 878
N+R +P E +L FPDD FP S YK +GN++ V V
Sbjct: 270 NIRRLTPRECARLQGFPDDFIFPG--SKTQLYKQIGNAVPVPVA 311
Score = 40.0 bits (94), Expect = 0.006
Identities = 17/44 (38%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 1174 NLRYFSPDEIRKLMCFPDECRFPPDCSDKSRYKLLGNSINVHVV 1217
N+R +P E +L FPD+ FP S YK +GN++ V V
Sbjct: 270 NIRRLTPRECARLQGFPDDFIFPG--SKTQLYKQIGNAVPVPVA 311
>gnl|CDD|233085 TIGR00675, dcm, DNA-methyltransferase (dcm). All proteins in this
family for which functions are known are DNA-cytosine
methyltransferases. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 315
Score = 40.0 bits (94), Expect = 0.006
Identities = 22/120 (18%), Positives = 45/120 (37%), Gaps = 9/120 (7%)
Query: 1098 VTEIARTNEREAKREDISPNVTGANQRDGSVNALGTNENAGNSVTTTRTNQNEESSVNTL 1157
++E + G ++ GS + + +++ + +
Sbjct: 198 LSEEK--KNGLLLLLENMRKKEGTGEQIGSFYNRESKSSIIRTLSARGYTFVKGGKSVLI 255
Query: 1158 ETNQNEATLLQELKRLNLRYFSPDEIRKLMCFPDECRFPPDCSDKSRYKLLGNSINVHVV 1217
+++ ++RL P E +L FPD+ +FP SD YK GN++ V V+
Sbjct: 256 VPHKSTVVHPGRIRRLT-----PRECARLQGFPDDFKFPV--SDSQLYKQAGNAVVVPVI 308
Score = 38.1 bits (89), Expect = 0.026
Identities = 24/116 (20%), Positives = 45/116 (38%), Gaps = 8/116 (6%)
Query: 763 ARTNESEAKREDISPNVMGAYQKDGSVTALGTNENAGNSVTTTRTNQNEENGVNTLLANQ 822
+ N E++ Q GS + + +++ + ++ ++
Sbjct: 201 EKKNGLLLLLENMRKKEGTGEQ-IGSFYNRESKSSIIRTLSARGYTFVKGGKSVLIVPHK 259
Query: 823 NEATLLQELKRLNLRYFSPDEIRKLMCFPDDCRFPPDCSDKSRYKLLGNSINVHVV 878
+ ++RL P E +L FPDD +FP SD YK GN++ V V+
Sbjct: 260 STVVHPGRIRRLT-----PRECARLQGFPDDFKFPV--SDSQLYKQAGNAVVVPVI 308
Score = 36.5 bits (85), Expect = 0.067
Identities = 17/44 (38%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 598 NLRYFSPDEIRKLMCFPDECQFPPDCSDKARYKLLGNSINVHVV 641
+R +P E +L FPD+ +FP SD YK GN++ V V+
Sbjct: 267 RIRRLTPRECARLQGFPDDFKFPV--SDSQLYKQAGNAVVVPVI 308
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 38.8 bits (90), Expect = 0.023
Identities = 87/412 (21%), Positives = 149/412 (36%), Gaps = 74/412 (17%)
Query: 424 EGTGSVLSNLGDMTHIEDIIEKCKHLKQQTDIS--STHETKAKKMRLNEEAQTQLSGEGE 481
GTG LG EDI L + D+ + E A + L+E +L +
Sbjct: 3814 SGTG-----LGSGVGAEDI---TNTLNEDDDLEELANEEDTANQSDLDESEARELESDMN 3865
Query: 482 KKTHDEMVKDAQNR-ADLEKKILDERVKDAQNRVDLEKNPEETVNDASNSNVITTNITEI 540
T D +V + +N ++ E + LDE V D DL + E + D N ++ E
Sbjct: 3866 GVTKDSVVSENENSDSEEENQDLDEEVNDIPE--DLSNSLNEKLWDEPNEE----DLLET 3919
Query: 541 NQNETKSKHIARTNESEAKREEIAPNATGAYQNQENSVNTLLANQNEATLLQELKRLNLR 600
Q + A NES+ +E A QE ++ + E++
Sbjct: 3920 EQKSNEQS--AANNESDLVSKEDDNKALEDKDRQEK--EDEEEMSDDVGIDDEIQ----- 3970
Query: 601 YFSPDEIRKLMCFPDECQFPPDCSDKARYKLLGNSINVHVVAYCICLMLCEPAPM-IDNS 659
+I++ + Q PP+ D L P + +D
Sbjct: 3971 ----PDIQE-----NNSQPPPENED-----------------------LDLPEDLKLDEK 3998
Query: 660 STDETKAKKIKLDVEDTETQFGDEGEREILDEMVKDAQNRVDLEKK-TLDEKVNDTLNQD 718
D +K D+ED + + DE + E E + Q+ LE+ TLDE + QD
Sbjct: 3999 EGDVSK----DSDLEDMDMEAADENKEEADAEKDEPMQDEDPLEENNTLDEDI----QQD 4050
Query: 719 DLVEKELLNGKVND---TLNKANSKDITTDVTGTNQNEAKSKQVTDIARTNESEAKREDI 775
D + + K+N+ N +++ T D +++ + + D A N + +
Sbjct: 4051 DFSDLAEDDEKMNEDGFEENVQENEESTEDGVKSDEELEQGEVPEDQAIDNHPKMDAKST 4110
Query: 776 SPNVMGAYQKDGSVTALGTNENAG--NSVTTTRTNQNEENGVNTLLANQNEA 825
+ A +++ +G NE G + V T E V + EA
Sbjct: 4111 FASA-EADEENTDKGIVGENEELGEEDGVRGNGTADGEFEQVQEDTSTPKEA 4161
Score = 37.7 bits (87), Expect = 0.057
Identities = 23/124 (18%), Positives = 49/124 (39%), Gaps = 7/124 (5%)
Query: 963 HYAEGTGSVLSNLGDMTQIEEIIEKCKHLKQQIDNSSTDETKAKKIKLDVEDT-----ET 1017
H E S D ++ + E + Q + N+ D+ K+ T
Sbjct: 4186 HEWEDLTESQSQAFDDSEFMHVKEDEEEDLQALGNAEKDQIKSIDRDESANQNPDSMNST 4245
Query: 1018 QFGDEGEREILDEMVKDAQNRVNLEKKTLDEKVND--TLNQDDLVEKELLNEKVNDTLNK 1075
++ E+ D+ ++D Q+ ++++ D + ++NQ + V + +E + D L
Sbjct: 4246 NIAEDEADEVGDKQLQDGQDISDIKQTGEDTLPTEFGSINQSEKVFELSEDEDIEDELPD 4305
Query: 1076 ANSK 1079
N K
Sbjct: 4306 YNVK 4309
Score = 31.5 bits (71), Expect = 3.8
Identities = 34/157 (21%), Positives = 58/157 (36%), Gaps = 5/157 (3%)
Query: 1011 DVEDTETQFGDEGEREILDEMVKDAQNRVNLEKK-TLDEKVNDTLNQDDLVEKELLNEKV 1069
D+ED + + DE + E E + Q+ LE+ TLDE + D + E +NE
Sbjct: 4007 DLEDMDMEAADENKEEADAEKDEPMQDEDPLEENNTLDEDIQQDDFSDLAEDDEKMNEDG 4066
Query: 1070 NDTLNKANSKDITTNVTGTNQNEAKSKHVTEIARTNEREAKREDISPNVTGANQRDGSVN 1129
+ + N + V + E + A N + + + A++ +
Sbjct: 4067 FEENVQENEESTEDGVKSDEELEQGEVPEDQ-AIDNHPKMDAKSTFASAE-ADEENTDKG 4124
Query: 1130 ALGTNENAG--NSVTTTRTNQNEESSVNTLETNQNEA 1164
+G NE G + V T E V + EA
Sbjct: 4125 IVGENEELGEEDGVRGNGTADGEFEQVQEDTSTPKEA 4161
Score = 31.1 bits (70), Expect = 5.4
Identities = 14/66 (21%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 677 ETQFGDEGEREILDEMVKDAQNRVDLEKKTLDEKVND--TLNQDDLVEKELLNGKVNDTL 734
T ++ E+ D+ ++D Q+ D+++ D + ++NQ + V + + + D L
Sbjct: 4244 STNIAEDEADEVGDKQLQDGQDISDIKQTGEDTLPTEFGSINQSEKVFELSEDEDIEDEL 4303
Query: 735 NKANSK 740
N K
Sbjct: 4304 PDYNVK 4309
>gnl|CDD|223348 COG0270, Dcm, Site-specific DNA methylase [DNA replication,
recombination, and repair].
Length = 328
Score = 37.4 bits (87), Expect = 0.039
Identities = 10/35 (28%), Positives = 18/35 (51%)
Query: 297 SMLTRAGFRFQEFLLSPTQFGVPNSRTRYYLIAKR 331
L G+ + +L+ +GVP SR R +++ R
Sbjct: 133 KELEELGYGVEFNILNAADYGVPQSRERVFIVGFR 167
Score = 36.3 bits (84), Expect = 0.091
Identities = 22/112 (19%), Positives = 39/112 (34%), Gaps = 8/112 (7%)
Query: 769 EAKREDISPNVMGAYQKDGSVTALGTNENAGNSVTTTRTNQNEENGVNTLLANQNEATLL 828
+ + + N AL + + R + ++ T+ NE +
Sbjct: 212 NHEAKSLPKNKGERLPSLRWGEALTLSRRYKGKGSYIRLHPDKPA--PTVRGGGNERFI- 268
Query: 829 QELKRLNLRYFSPDEIRKLMCFPDDCRFPPDCSDKSRYKLLGNSINVHVVAY 880
L R + E +L FPDD FP S +Y+ +GNS+ +
Sbjct: 269 ---HPLEDRELTVREAARLQGFPDDFVFPG--SKTDQYRQIGNSVPPLLAEA 315
Score = 35.5 bits (82), Expect = 0.17
Identities = 22/113 (19%), Positives = 41/113 (36%), Gaps = 8/113 (7%)
Query: 1107 REAKREDISPNVTGANQRDGSVNALGTNENAGNSVTTTRTNQNEESSVNTLETNQNEATL 1166
R + + + N AL + + R + ++ + T+ NE +
Sbjct: 211 RNHEAKSLPKNKGERLPSLRWGEALTLSRRYKGKGSYIRLHPDKPA--PTVRGGGNERFI 268
Query: 1167 LQELKRLNLRYFSPDEIRKLMCFPDECRFPPDCSDKSRYKLLGNSINVHVVAY 1219
L R + E +L FPD+ FP S +Y+ +GNS+ +
Sbjct: 269 ----HPLEDRELTVREAARLQGFPDDFVFPG--SKTDQYRQIGNSVPPLLAEA 315
Score = 34.3 bits (79), Expect = 0.34
Identities = 21/158 (13%), Positives = 40/158 (25%), Gaps = 25/158 (15%)
Query: 489 VKDAQNRADLEKKILDERVKDAQNRVDLEKNPEETVNDASNSNVIT---TNITEINQNET 545
+ L++ + + + + + E
Sbjct: 180 PLPLGRKKTLKEALKNNDLPETDELYLSRDLRNHEAKSLPKNKGERLPSLRWGEALTLSR 239
Query: 546 KSKHIARTNESEAKREEIAPNATGAYQNQENSVNTLLANQNEATLLQELKRLNLRYFSPD 605
+ K S + P T E + L R +
Sbjct: 240 RYKGK----GSYIRLHPDKPAPTVRGGGNERFI----------------HPLEDRELTVR 279
Query: 606 EIRKLMCFPDECQFPPDCSDKARYKLLGNSINVHVVAY 643
E +L FPD+ FP S +Y+ +GNS+ +
Sbjct: 280 EAARLQGFPDDFVFPG--SKTDQYRQIGNSVPPLLAEA 315
>gnl|CDD|234141 TIGR03185, DNA_S_dndD, DNA sulfur modification protein DndD. This
model describes the DndB protein encoded by an operon
associated with a sulfur-containing modification to DNA.
The operon is sporadically distributed in bacteria, much
like some restriction enzyme operons. DndD is described
as a putative ATPase. The small number of examples known
so far include species from among the Firmicutes,
Actinomycetes, Proteobacteria, and Cyanobacteria [DNA
metabolism, Restriction/modification].
Length = 650
Score = 37.0 bits (86), Expect = 0.068
Identities = 29/127 (22%), Positives = 52/127 (40%), Gaps = 4/127 (3%)
Query: 437 THIEDIIEKC-KHLKQQTDISSTHETKAKKMRLN-EEAQTQLSGEGEKKTHDEMVKDAQN 494
+ I IE LK+Q++ + +R EEAQ L EKK E +
Sbjct: 205 SSILSEIEALEAELKEQSEKYEDLAQEIAHLRNELEEAQRSLE-SLEKKFRSEGGDLFEE 263
Query: 495 RADLEKKILDERVKDAQNRVDLEKNPEETVNDASNSNVITTNITEINQNETKSKHIARTN 554
R LE+++ + NR L + + + N++ + ++ Q E +S+ T
Sbjct: 264 REQLERQLKEIEAARKANRAQLRELAADPLPLLLIPNLLDSTKAQL-QKEEQSQQNQLTQ 322
Query: 555 ESEAKRE 561
E +R+
Sbjct: 323 EELEERD 329
>gnl|CDD|222169 pfam13485, Peptidase_MA_2, Peptidase MA superfamily.
Length = 128
Score = 34.8 bits (80), Expect = 0.080
Identities = 9/32 (28%), Positives = 12/32 (37%), Gaps = 5/32 (15%)
Query: 38 LIPHEYAHYHLDLTATAEKFRLSGLPYTWLTE 69
++ HE AH +G WLTE
Sbjct: 28 VLAHELAHV-----VLGNLVGGNGNLPRWLTE 54
>gnl|CDD|240419 PTZ00440, PTZ00440, reticulocyte binding protein 2-like protein;
Provisional.
Length = 2722
Score = 36.7 bits (85), Expect = 0.11
Identities = 42/224 (18%), Positives = 82/224 (36%), Gaps = 41/224 (18%)
Query: 979 TQIEEIIEKCKHLKQQIDNSSTDETKAKKIKLDVEDTETQFGDEGEREILDEMVKDAQNR 1038
QIE+ +E K+ I+ D T + KLD E E + K ++
Sbjct: 959 MQIEKTLEYYDKSKENIN--GNDGTHLE--KLDKEKDEWEH------------FKSEIDK 1002
Query: 1039 VNLEKKTLDEKVNDTLNQ--DDLVE--KELLNEKVNDTLNK-----ANSKDITTNVTG-- 1087
+N+ L++K++D + + DD++E +L+ EK + K + + + T ++
Sbjct: 1003 LNVNYNILNKKIDDLIKKQHDDIIELIDKLIKEKGKEIEEKVDQYISLLEKMKTKLSSFH 1062
Query: 1088 TNQNEAKSKHVTEIARTNEREAKREDISPNVTGANQR---------DGSVNALGTNENAG 1138
N + K K+ E K E + + + + VNA
Sbjct: 1063 FNIDIKKYKNPKIKEEIKLLEEKVEALLKKIDENKNKLIEIKNKSHEHVVNADKEKNKQT 1122
Query: 1139 NSVTTTRTN-----QNEESSVNTLETNQNEATLLQELKRLNLRY 1177
+ + + E ++ LE E L E+ + + Y
Sbjct: 1123 EHYNKKKKSLEKIYKQMEKTLKELENMNLEDITLNEVNEIEIEY 1166
Score = 30.6 bits (69), Expect = 7.8
Identities = 31/169 (18%), Positives = 64/169 (37%), Gaps = 31/169 (18%)
Query: 436 MTHIEDIIEKCKH---LKQQTDISSTHETKAKKMRLNEEAQTQLSGEGEKKTHDEMVKDA 492
+ I+ +I++ K IS + K K + KK + +K+
Sbjct: 1026 IELIDKLIKEKGKEIEEKVDQYISLLEKMKTK-------LSSFHFNIDIKKYKNPKIKE- 1077
Query: 493 QNRADLEKKILDERVKDAQNRVDLEKNPEETVNDASNSNVITTNITEINQNETKSKHIAR 552
E K+L+E+V+ ++D KN + + S+ +V+ + + Q E +K
Sbjct: 1078 ------EIKLLEEKVEALLKKIDENKNKLIEIKNKSHEHVVNADKEKNKQTEHYNK---- 1127
Query: 553 TNESEAKREEIAPNATGAYQNQENSVNTLLANQNEATLLQELKRLNLRY 601
K++ + Y+ E ++ L E L E+ + + Y
Sbjct: 1128 ------KKKSLEK----IYKQMEKTLKELENMNLEDITLNEVNEIEIEY 1166
>gnl|CDD|226400 COG3883, COG3883, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 265
Score = 34.7 bits (80), Expect = 0.25
Identities = 16/101 (15%), Positives = 44/101 (43%), Gaps = 8/101 (7%)
Query: 693 VKDAQNRVDLEKKTLDEKVNDTLNQDDLVEKEL--LNGKVNDTLNKANSKDITTDVTGTN 750
V A ++ + D K+++ + ++ E+ L+ ++ + +K + D +
Sbjct: 24 VFAALLSDKIQNQ--DSKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAE 81
Query: 751 QNEAKSKQVTDIARTNESEAKREDISPNVMGAYQKDGSVTA 791
+ + + IA E+ +R+++ A Q +G+ T+
Sbjct: 82 IKKLQKE----IAELKENIVERQELLKKRARAMQVNGTATS 118
Score = 30.8 bits (70), Expect = 3.8
Identities = 12/85 (14%), Positives = 36/85 (42%), Gaps = 8/85 (9%)
Query: 1032 VKDAQNRVNLEKKTLDEKVNDTLNQDDLVEKEL--LNEKVNDTLNKANSKDITTNVTGTN 1089
V A ++ + D K+++ + ++ E+ L+ ++ + +K + + +
Sbjct: 24 VFAALLSDKIQNQ--DSKLSELQKEKKNIQNEIESLDNQIEEIQSKIDELQKEIDQSKAE 81
Query: 1090 QNEAKSKHVTEIARTNEREAKREDI 1114
+ + EIA E +R+++
Sbjct: 82 IKKLQK----EIAELKENIVERQEL 102
>gnl|CDD|224263 COG1344, FlgL, Flagellin and related hook-associated proteins [Cell
motility and secretion].
Length = 360
Score = 34.7 bits (80), Expect = 0.30
Identities = 37/178 (20%), Positives = 59/178 (33%), Gaps = 16/178 (8%)
Query: 653 APMIDNSSTDETKAKKIKLDVEDTETQFGDEGEREILDEMVKDAQNRVDLEKKTLDEKVN 712
P ++ ET IK + G LD + L DE ++
Sbjct: 143 KPFDFQNAGGET----IKGSFNSDSSGTVSVG----LDITNTGDLSFTSLGTTAKDEPID 194
Query: 713 --DTLNQDDLVEKELLNGKVNDTLNKANSKDITTDVTGTNQNEAKSKQVTDIARTNESEA 770
D + N +L KA T G N + + + D + A
Sbjct: 195 AGDVTAGPTNLFGAGANAADGASLGKALDAATTNTQIGANVGQTTTLNIND-GNVMTASA 253
Query: 771 KREDISPNVMGAYQKDGSVTALGTNENAGNSVTTTRTN----QNEENGVNTLLANQNE 824
P A DG+ ALGT ++A +++T+ R QN L+NQ++
Sbjct: 254 AGALADPGSSVA-TADGAQAALGTIDSALDNITSARAELGAVQNRLESAINNLSNQSD 310
>gnl|CDD|220262 pfam09485, CRISPR_Cse2, CRISPR-associated protein Cse2
(CRISPR_cse2). Clusters of short DNA repeats with
non-homologous spacers, which are found at regular
intervals in the genomes of phylogenetically distinct
prokaryotic species, comprise a family with recognisable
features. This family is known as CRISPR (short for
Clustered, Regularly Interspaced Short Palindromic
Repeats). A number of protein families appear only in
association with these repeats and are designated Cas
(CRISPR-Associated) proteins. This family of proteins,
represented by CT1973 from Chlorobaculum tepidum, is
encoded by genes found in the CRISPR/Cas subtype Ecoli
regions of many bacteria (most of which are mesophiles),
and not in Archaea. It is designated Cse2.
Length = 143
Score = 33.1 bits (76), Expect = 0.31
Identities = 20/111 (18%), Positives = 32/111 (28%), Gaps = 18/111 (16%)
Query: 295 TTSMLTRAGFRFQEFLLSPTQFGVPNSRTRYYLIA------KRSPAAHSSEASFCFETSS 348
+ + + L+A K+ P H+ S
Sbjct: 11 GPDPVLPEAAFLYVAPPALKEDAREAEEEALALVAALLAHHKQDPPGHTFARS------- 63
Query: 349 ELMTELPKLKSKTCNPLLSRMTLHSILDSTDPSDDLYR-RYLVSDKDLLRR 398
L L +L+ +S +L + P + L R R LV LLR
Sbjct: 64 -LGRALARLRQDGDKSDVSERRFRQLLRADTPDELLRRLRRLVR---LLRG 110
>gnl|CDD|237256 PRK12901, secA, preprotein translocase subunit SecA; Reviewed.
Length = 1112
Score = 35.0 bits (81), Expect = 0.32
Identities = 25/105 (23%), Positives = 46/105 (43%), Gaps = 22/105 (20%)
Query: 977 DMTQIEEIIEKCKHLKQQIDNSSTDETKAKKIKLDVEDTETQFGDEGEREILDEMVKDAQ 1036
D+ +I+ I+EK K +++ S DE +AK + ++ + E V D
Sbjct: 16 DLKEIQPIVEKIKAEYPELEALSNDELRAKTDEF--------------KQYIKEAVADID 61
Query: 1037 NRVN------LEKKTLDEKVNDTLNQDDLVEKELLNEKVNDTLNK 1075
++ +E +DE+ D Q D +EKE E + L++
Sbjct: 62 AKIEELKAEAIESLDIDER-EDIYAQIDKLEKE-AYEILEKVLDE 104
>gnl|CDD|222819 PHA01077, PHA01077, putative lower collar protein.
Length = 251
Score = 33.2 bits (75), Expect = 0.64
Identities = 22/128 (17%), Positives = 51/128 (39%), Gaps = 1/128 (0%)
Query: 455 ISSTHETKAKKMRLNEEAQTQLSGEGEKKTHDEMVKDAQNRADLEKKILDERVKDAQNRV 514
+ THE + + E + L +G + +++ + ++ LD NR
Sbjct: 101 VCITHEDYLNVVYSSSEVEKYLQSQGFTEHNEDTTNNTDETSNQNATSLDNSTGMTANRN 160
Query: 515 DLEKNPEETVN-DASNSNVITTNITEINQNETKSKHIARTNESEAKREEIAPNATGAYQN 573
P+ VN D N+ + + I+ +T +K +N++ + + NA G
Sbjct: 161 AYVSLPQSEVNIDVDNTTLRFADNNTIDNGKTVNKSSNESNQNAKRNQNQKGNAKGTQFT 220
Query: 574 QENSVNTL 581
++ ++ +
Sbjct: 221 KQYLIDNI 228
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 34.0 bits (77), Expect = 0.71
Identities = 53/313 (16%), Positives = 117/313 (37%), Gaps = 36/313 (11%)
Query: 444 EKCKHLKQQTDISSTHETKAKKMRLNEE------AQTQLSGEGEKKTHDEMVKDAQNRAD 497
E+ K ++Q + + KA++++ EE A+ E +KK +E K ++
Sbjct: 1630 EEKKKVEQLKKKEAEEKKKAEELKKAEEENKIKAAEEAKKAEEDKKKAEEAKKAEEDEKK 1689
Query: 498 LEKKILDE-----RVKDAQNRVDLEKNPEETVNDASNSNVITTNITEINQNETKSKHIAR 552
+ + E + ++ + + EK E + A N I + E K K
Sbjct: 1690 AAEALKKEAEEAKKAEELKKKEAEEKKKAEELKKAEEENKIKAEEAKKEAEEDKKK---- 1745
Query: 553 TNESEAKREEIAPNATGAYQNQENSVNTLLANQNEATLLQELKRLNLRYFSPDEIRKLMC 612
EAK++E + +E + + EA + +EL + + + +K+
Sbjct: 1746 --AEEAKKDEEEKKKIAHLKKEEEKKAEEIRKEKEAVIEEELDEEDEKRRMEVD-KKI-- 1800
Query: 613 FPDECQFPPDCSDKARYKLLGNSINVHVVAYCICLMLCEPAPMIDNSSTDETKAKKIKLD 672
D D + G V+ + + D+ + +A +
Sbjct: 1801 --------KDIFDNFANIIEGGKEGNLVINDSKEMEDSAIKEVADSKNMQLEEADAFEKH 1852
Query: 673 VEDTETQFGDEGEREILDEMVKDAQNRVDLEKKTLDEKVNDTLNQDDLVEKELLNGKVND 732
+ + G++G +E + K+ + D E++ + + +++DD+ E+E+ N +
Sbjct: 1853 KFNKNNENGEDGNKE--ADFNKEKDLKEDDEEEIEEADEIEKIDKDDI-EREIPNNNM-- 1907
Query: 733 TLNKANSKDITTD 745
+ DI D
Sbjct: 1908 ---AGKNNDIIDD 1917
>gnl|CDD|188306 TIGR03319, RNase_Y, ribonuclease Y. Members of this family are RNase
Y, an endoribonuclease. The member from Bacillus
subtilis, YmdA, has been shown to be involved in turnover
of yitJ riboswitch [Transcription, Degradation of RNA].
Length = 514
Score = 33.4 bits (77), Expect = 0.94
Identities = 36/160 (22%), Positives = 70/160 (43%), Gaps = 29/160 (18%)
Query: 980 QIEEIIEKCKHLKQQIDNSSTDETKAKK--IKLDVEDTETQFGDEGEREILDEM--VKDA 1035
E+ + + L ++I + E + K L+ ++ + E ERE+ + ++
Sbjct: 22 IAEKKLGSAEELAKRIIEEAKKEAETLKKEALLEAKEEVHKLRAELERELKERRNELQRL 81
Query: 1036 QNRVNLEKKTLDEKVNDTLNQDDLVEK---ELLNEKVN-DTLNK------ANSKDITTNV 1085
+ R+ ++TLD K+ +++ +EK EL N++ N D + A ++ +
Sbjct: 82 ERRLLQREETLDRKMESLDKKEENLEKKEKELSNKEKNLDEKEEELEELIAEQREELERI 141
Query: 1086 TGTNQNEAK----------SKHVTEIA---RTNEREAKRE 1112
+G Q EAK ++H E A + E EAK E
Sbjct: 142 SGLTQEEAKEILLEEVEEEARH--EAAKLIKEIEEEAKEE 179
>gnl|CDD|109486 pfam00430, ATP-synt_B, ATP synthase B/B' CF(0). Part of the CF(0)
(base unit) of the ATP synthase. The base unit is
thought to translocate protons through membrane (inner
membrane in mitochondria, thylakoid membrane in plants,
cytoplasmic membrane in bacteria). The B subunits are
thought to interact with the stalk of the CF(1)
subunits. This domain should not be confused with the ab
CF(1) proteins (in the head of the ATP synthase) which
are found in pfam00006.
Length = 132
Score = 31.5 bits (72), Expect = 1.1
Identities = 14/67 (20%), Positives = 28/67 (41%), Gaps = 5/67 (7%)
Query: 452 QTDISSTHETKAKKMRLNEEAQTQLSGEGEKKTHDEMVKDAQNRADLEKKILDERVKDAQ 511
+I E + L EA+ QL + E++ +A+ A +K+ +E + +AQ
Sbjct: 36 ANNIKEAEERLKQAAALLAEAEQQL--AQARAEASEIINNAKKEA---QKLKEEILAEAQ 90
Query: 512 NRVDLEK 518
+
Sbjct: 91 KDAERLL 97
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 32.8 bits (75), Expect = 1.4
Identities = 30/203 (14%), Positives = 71/203 (34%), Gaps = 13/203 (6%)
Query: 980 QIEEIIEKCKHLKQQIDNSSTDETKA----KKIKLDVEDTETQFGDEGEREILDEMVKDA 1035
+IEE+ + L+++++ + + +++K +E + + ERE L E ++
Sbjct: 296 EIEELEGEISLLRERLEELENELEELEERLEELKEKIEALKEEL---EERETLLEELEQL 352
Query: 1036 QNRVNLEKKTLDEKVNDTLNQDDLVEKELLNEKVNDTLNKANSKDITTNVTGTNQNEAKS 1095
+ K+ L+EK L ++ E L E++ + + +
Sbjct: 353 LAELEEAKEELEEK-LSALLEELEELFEALREELAELEAELAEIRNELEELKREIESLEE 411
Query: 1096 KHVTEIARTNEREAKREDISPNVTGANQRDGSVNA-LGTNENAGNSVTTTRTNQNEESSV 1154
+ R + + + +++ + +N L E + E +
Sbjct: 412 RLERLSERLEDLKEELKELEAELEELQTELEELNEELEELEEQLEELRDRLKELERELA- 470
Query: 1155 NTLETNQNEATLLQELKRLNLRY 1177
E + L +EL L R
Sbjct: 471 ---ELQEELQRLEKELSSLEARL 490
>gnl|CDD|115185 pfam06513, DUF1103, Repeat of unknown function (DUF1103). This
family consists of several repeats of around 30 residues
in length which are found specifically in
mature-parasite-infected erythrocyte surface antigen
proteins from Plasmodium falciparum. This family often
found in conjunction with pfam00226.
Length = 215
Score = 31.4 bits (70), Expect = 2.3
Identities = 34/138 (24%), Positives = 66/138 (47%), Gaps = 8/138 (5%)
Query: 989 KHLKQQIDNSSTDETKAKKIKLDVEDTETQFGDEGE-REILDEMVKDAQNRVNLEKKTLD 1047
K +K++++ ++ K KK+K +++ +T+ D+ + EI+ E VK+ ++K+ D
Sbjct: 30 KEIKEKVEKRVKEKCK-KKVKKGIKENDTEGNDKVKGPEIIIEEVKE-----EIKKQVED 83
Query: 1048 E-KVNDTLNQDDLVEKELLNEKVNDTLNKANSKDITTNVTGTNQNEAKSKHVTEIARTNE 1106
K NDT D + E++ E+V + + K I N T N + +TE +
Sbjct: 84 GIKENDTEGNDKVKGPEIITEEVKEEIKKQVEDGIKENDTEGNDKVKGPEIITEEVKEEI 143
Query: 1107 REAKREDISPNVTGANQR 1124
++ E I N T +
Sbjct: 144 KKQVEEGIKENDTEGKDK 161
Score = 29.4 bits (65), Expect = 9.4
Identities = 28/119 (23%), Positives = 51/119 (42%), Gaps = 1/119 (0%)
Query: 1002 ETKAKKIKLDVEDTETQFGDEGEREILDEMVKDAQNRVNLEKKTLDE-KVNDTLNQDDLV 1060
E ++IK VED + EG ++ + + + ++K+ D K NDT D +
Sbjct: 71 EEVKEEIKKQVEDGIKENDTEGNDKVKGPEIITEEVKEEIKKQVEDGIKENDTEGNDKVK 130
Query: 1061 EKELLNEKVNDTLNKANSKDITTNVTGTNQNEAKSKHVTEIARTNEREAKREDISPNVT 1119
E++ E+V + + K + I N T + +TE + ++ E I N T
Sbjct: 131 GPEIITEEVKEEIKKQVEEGIKENDTEGKDKLIGPEIITEEVKEEIKKQVEEGIKENDT 189
>gnl|CDD|223599 COG0525, ValS, Valyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 877
Score = 32.2 bits (74), Expect = 2.3
Identities = 22/131 (16%), Positives = 51/131 (38%), Gaps = 14/131 (10%)
Query: 980 QIEEIIEKCKHLKQQIDNSSTDETKAKKIKLDVEDTETQFGDEGEREILDEMVKDAQNRV 1039
++E+ +E + + + N E + + + T E + + D +
Sbjct: 758 ELEDRLEANEDDIKGLANLEELEILSPDPE-EPPVEVTAVVGGAELFLPLAGLID----L 812
Query: 1040 NLEKKTLDEKVNDTLNQDDLVEKELLNEKVNDTLNKANSKDITTNVTGTNQNEAKSKHVT 1099
E L++++ + D +EK+L NE + KA + + E +++
Sbjct: 813 AAELARLEKELEKLEKEIDRIEKKLSNEGF---VAKAPEEVVEKEK------EKLAEYQV 863
Query: 1100 EIARTNEREAK 1110
++A+ ER A
Sbjct: 864 KLAKLEERLAV 874
>gnl|CDD|216193 pfam00921, Lipoprotein_2, Borrelia lipoprotein. This family of
lipoproteins is found in Borrelia spirochetes. The
function of these proteins is uncertain.
Length = 174
Score = 30.5 bits (69), Expect = 3.7
Identities = 11/45 (24%), Positives = 16/45 (35%)
Query: 502 ILDERVKDAQNRVDLEKNPEETVNDASNSNVITTNITEINQNETK 546
IL VK + L E+ A+ + N E+N K
Sbjct: 62 ILQAIVKSKEADAQLGAGIEKAAGAAAIAFAKGGNKAELNGAAAK 106
>gnl|CDD|240412 PTZ00420, PTZ00420, coronin; Provisional.
Length = 568
Score = 31.5 bits (71), Expect = 3.7
Identities = 23/97 (23%), Positives = 40/97 (41%), Gaps = 3/97 (3%)
Query: 1058 DLVEKELLNEKVNDTLNKANSKDITTNVTGTNQNEAKSKHVTEIARTNEREAKREDISPN 1117
EKELL EK + ANS + + N + E+ +TNE E +
Sbjct: 460 SFKEKELLTEKGGAQFSSANSLERGADEDYLIVNGTNEPYEEEVIKTNENENFPLENESP 519
Query: 1118 VTGANQRDGSVNALGTNENAGNSVTTTRTNQNEESSV 1154
G G+ + L N++ N++ T ++E ++
Sbjct: 520 CDG--ISRGT-SELPVNDDDNNNLNRGNTLRSEGNNC 553
>gnl|CDD|219256 pfam06991, Prp19_bind, Splicing factor, Prp19-binding domain. This
family represents the C-terminus (approximately 300
residues) of proteins that are involved as binding
partners for Prp19 as part of the nuclear pore complex.
The family in Drosophila is necessary for pre-mRNA
splicing, and the human protein has been found in
purifications of the spliceosome. In the past this
family was thought, erroneously, to be associated with
microfibrillin.
Length = 277
Score = 31.0 bits (70), Expect = 4.0
Identities = 22/97 (22%), Positives = 43/97 (44%), Gaps = 8/97 (8%)
Query: 469 NEEAQTQLSGEGEKKTHDEMVKDAQNRADLEKKILDERVKDAQNRVDLEKNPEETVNDAS 528
+E + + + E + + + A+ R KI++E VK +LE T+ +A+
Sbjct: 50 IQEREREAAKEKALEEEAK--RKAEERKRETLKIVEEEVKK-----ELELKKRNTLLEAN 102
Query: 529 NSNVITTNITEINQNET-KSKHIARTNESEAKREEIA 564
+V T + E + E K + + R +REE+
Sbjct: 103 IDDVDTDDENEEEEYEAWKLRELKRIKRDREEREEME 139
>gnl|CDD|221952 pfam13166, AAA_13, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins. This family includes the
PrrC protein that is thought to be the active component
of the anticodon nuclease.
Length = 713
Score = 31.1 bits (71), Expect = 4.4
Identities = 20/93 (21%), Positives = 35/93 (37%), Gaps = 5/93 (5%)
Query: 979 TQIEEIIEKCKHLKQQI-DNSSTDETKAKKIKLDVEDTETQFGDEGEREILDEMVKDAQN 1037
+++++ EK + L+ +I E K + D E L K
Sbjct: 102 KELKKLEEKIEQLEAEIEKKEEELEKAKNKFLDKAWKKLAKKYDSNLSEAL----KGLNY 157
Query: 1038 RVNLEKKTLDEKVNDTLNQDDLVEKELLNEKVN 1070
+ N ++K L E + LN L+ E L K+
Sbjct: 158 KKNFKEKLLKELKSVILNASSLLSLEELKAKIK 190
>gnl|CDD|202096 pfam02029, Caldesmon, Caldesmon.
Length = 431
Score = 30.8 bits (69), Expect = 5.0
Identities = 30/117 (25%), Positives = 47/117 (40%), Gaps = 13/117 (11%)
Query: 415 FTKAYTHYAEGTGSVLSNLGDMTHIEDIIEKCKHLKQQTDISSTHETKAK----KMRLNE 470
F + E T S G EK K KQQ E K K + L E
Sbjct: 174 FMTHKLKHTENTFSRGGAEGAQVEAGKEFEKLKQ-KQQEAALELEELKKKREERRKVLEE 232
Query: 471 EAQTQLSGEGEKKTHDEMVKDAQNRADLEKKILDERVKDAQNRVDLEKNPEETVNDA 527
E Q + E ++K+ +E K L+++I R + A+ R +K PE+ +++
Sbjct: 233 EEQRRKQEEADRKSREEEEKRR-----LKEEIERRRAEAAEKR---QKVPEDGLSED 281
>gnl|CDD|227602 COG5277, COG5277, Actin and related proteins [Cytoskeleton].
Length = 444
Score = 30.9 bits (70), Expect = 5.3
Identities = 24/139 (17%), Positives = 44/139 (31%), Gaps = 21/139 (15%)
Query: 922 PSGDLYRRYLVSDKDLLRRFHVFDIVNRKASSTNCFTKAYTHYAEGTGSVLSNLGDMTQI 981
R Y + + + +IVN + C T + Y
Sbjct: 203 EKYPPSRGYNLKSELVEYSS---EIVN-EIKEEVCETDDESAYVS------------LDA 246
Query: 982 EEIIEKCKHLKQQI----DNSSTDETK-AKKIKLDVEDTETQFGDEGEREILDEMVKDAQ 1036
EE E+ + + + ET AK+ K + E +FG+E + + + K
Sbjct: 247 EEEFEEEEEKPAEKSTESTFQLSKETSIAKESKELPDGEEIEFGNEERFKAPEILFKPEL 306
Query: 1037 NRVNLEKKTLDEKVNDTLN 1055
LE+ ++ L
Sbjct: 307 PISGLEEAGKIDESKQELV 325
>gnl|CDD|225177 COG2268, COG2268, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 548
Score = 31.0 bits (70), Expect = 5.4
Identities = 19/113 (16%), Positives = 41/113 (36%), Gaps = 18/113 (15%)
Query: 460 ETKAKKMRLNEEAQTQLSGEGEKKTHDEMVKDAQNRADLEKKILDERVKDAQNRVDLEKN 519
ET+ + + A+ + E + ++ V Q+ LE + + RV + + + E
Sbjct: 284 ETRREAEQAEILAEQAIQEEKAQ--AEQEV---QHAKALEAREM--RVGLIERQKETELE 336
Query: 520 PEETVNDASNSNVITTNITEINQNETKSKHIARTNESEAKREEIAPNATGAYQ 572
P+E + Q + + + A N +EA + A +
Sbjct: 337 PQE-----------RSYFINAAQRQAQEEAKAAANIAEAIGAQAEAAVETARE 378
>gnl|CDD|224475 COG1559, COG1559, Aminodeoxychorismate lyase [Coenzyme transport and
metabolism].
Length = 342
Score = 30.3 bits (69), Expect = 5.8
Identities = 19/100 (19%), Positives = 37/100 (37%), Gaps = 13/100 (13%)
Query: 977 DMTQIEEIIEKCKHLKQQIDNSSTDETKA---KKIKLDVED---TETQFGDEGER--EIL 1028
+ QI + + + L +D + E A K K +E +T G +I+
Sbjct: 125 TLKQIAKKLAEAPVLDGVLDGLAIAEIAARLPKLDKERLEGYLFPDTYEFTRGTSAEDII 184
Query: 1029 DEMVKDAQNRVNLEKKTLDEK-----VNDTLNQDDLVEKE 1063
M+K +++ + + + L +VEKE
Sbjct: 185 KRMIKAMDKKLDEAWEKRADDLPGKTPYELLTLASIVEKE 224
>gnl|CDD|224192 COG1273, COG1273, Ku-homolog [Replication, recombination, and
repair].
Length = 278
Score = 30.4 bits (69), Expect = 6.4
Identities = 14/60 (23%), Positives = 28/60 (46%), Gaps = 3/60 (5%)
Query: 673 VEDTETQFGDEGEREILDEMVKDAQNRVDLEKKTLD-EKVNDTLNQD--DLVEKELLNGK 729
V + F + +I EM++ A+ +D + T D ++ D + +L+E +L K
Sbjct: 171 VRSPDEYFPGIPDIKIDPEMLELAKQLIDKKTGTFDPDEYEDRYQEALMELIEAKLEGRK 230
>gnl|CDD|226894 COG4499, COG4499, Predicted membrane protein [Function unknown].
Length = 434
Score = 30.5 bits (69), Expect = 6.7
Identities = 19/63 (30%), Positives = 32/63 (50%), Gaps = 7/63 (11%)
Query: 439 IEDIIEKCKHLKQQTDISSTHETKAKKMRLNEEAQTQLSGEGEKKTHDEMVKDAQNRADL 498
++D +K +K +TD S E KAK E+ + + E EKK ++ +D + R
Sbjct: 378 LQDYTKKLGEVKDETDASEEAEAKAK----EEKLKQE---ENEKKQKEQADEDKEKRQKD 430
Query: 499 EKK 501
E+K
Sbjct: 431 ERK 433
>gnl|CDD|235219 PRK04098, PRK04098, sec-independent translocase; Provisional.
Length = 158
Score = 29.3 bits (66), Expect = 6.7
Identities = 26/122 (21%), Positives = 45/122 (36%), Gaps = 29/122 (23%)
Query: 980 QIEEIIEKCKHLKQQIDNSSTDETKAKKIKLDVEDTETQFGDEGEREILDEMVKDAQNRV 1039
IEEI E+ K++ +++ K K E LD++ A+N
Sbjct: 55 NIEEIKEEALKYKKEFESAVESLKKKLKF-----------------EELDDLKITAEN-- 95
Query: 1040 NLEKKTLDEKVNDTLNQDDLVEKELLN----EKVNDTLNKANSK--DITTNVTGTNQNEA 1093
E K++ + + D + L E + N E N+T S + V +N+
Sbjct: 96 --EIKSIQDLLQD--YKKSLEEDTIPNHLNEEVSNETKLTQESSSDESPKEVKLATKNKT 151
Query: 1094 KS 1095
K
Sbjct: 152 KK 153
>gnl|CDD|182907 PRK11023, PRK11023, outer membrane lipoprotein; Provisional.
Length = 191
Score = 29.2 bits (66), Expect = 8.9
Identities = 19/72 (26%), Positives = 33/72 (45%), Gaps = 14/72 (19%)
Query: 706 TLDEKVNDTLNQDDLVEKE------------LLNGKVNDTLNKANSKDITTDVTGTNQ-- 751
TL+ +VN+ L++D+ ++KE LL G+ + +K I V G N+
Sbjct: 49 TLELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQSPNAELSERAKQIAMGVEGVNEVY 108
Query: 752 NEAKSKQVTDIA 763
NE + Q +
Sbjct: 109 NEIRQGQPIGLG 120
>gnl|CDD|213709 TIGR02393, RpoD_Cterm, RNA polymerase sigma factor RpoD, C-terminal
domain. This model represents the well-conserved
C-terminal region of the major, essential sigma factor of
most bacteria. Members of this clade show considerable
variability in domain architecture and molecular weight,
as well as in nomenclature: RpoD in E. coli and other
Proteobacteria, SigA in Bacillus subtilis and many other
Gram-positive bacteria, HrdB in Streptomyces, MysA in
Mycobacterium smegmatis, etc [Transcription,
Transcription factors].
Length = 238
Score = 29.6 bits (67), Expect = 9.4
Identities = 28/110 (25%), Positives = 50/110 (45%), Gaps = 22/110 (20%)
Query: 980 QIEEIIEKCKHLKQQIDNSSTDETKAKKIKLDVEDTETQFGDEGEREILDEMVKDAQNRV 1039
I ++I+ + L Q++ TDE A+++ + E REI K AQ +
Sbjct: 85 TINKLIKAERQLTQELGREPTDEELAERMGMPAEKV---------REIK----KIAQEPI 131
Query: 1040 NLEKKTLDEK-------VNDT--LNQDDLVEKELLNEKVNDTLNKANSKD 1080
+LE +E+ + DT + DD KELL E++++ L ++
Sbjct: 132 SLETPIGEEEDSFLGDFIEDTSIESPDDYAAKELLREQLDEVLETLTERE 181
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
0.315 0.131 0.376
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 59,910,648
Number of extensions: 5804017
Number of successful extensions: 6050
Number of sequences better than 10.0: 1
Number of HSP's gapped: 6009
Number of HSP's successfully gapped: 132
Length of query: 1232
Length of database: 10,937,602
Length adjustment: 108
Effective length of query: 1124
Effective length of database: 6,147,370
Effective search space: 6909643880
Effective search space used: 6909643880
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 65 (28.8 bits)