RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2956
(251 letters)
>gnl|CDD|224557 COG1643, HrpA, HrpA-like helicases [DNA replication, recombination,
and repair].
Length = 845
Score = 251 bits (642), Expect = 5e-78
Identities = 95/183 (51%), Positives = 117/183 (63%), Gaps = 13/183 (7%)
Query: 14 QYFDNAPLMNVPGRTHPVEIFYTPEPERDY-LEAAIRTVVQIHMCEEVEGDVLLFLTGQE 72
YF NAP++ + GRT+PVEI Y PE E DY L AI V IH+ E G +L+FL GQ
Sbjct: 212 AYFGNAPVIEIEGRTYPVEIRYLPEAEADYILLDAIVAAVDIHLREG-SGSILVFLPGQR 270
Query: 73 EIEEACKRIKKEIDNLGPEAGELKCIPLYSTLPPNLQQRIFEAAPANKPNGGIGRKVVVS 132
EIE + ++K LG + L+ +PLY L Q R+FE AP K RKVV++
Sbjct: 271 EIERTAEWLEK--AELGDD---LEILPLYGALSAEEQVRVFEPAPGGK------RKVVLA 319
Query: 133 TNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTRPGK 192
TNIAETSLTI G+ +VID G AK+K Y+PR + L PISKASA QRAGRAGRT PG
Sbjct: 320 TNIAETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLETEPISKASADQRAGRAGRTGPGI 379
Query: 193 CFR 195
C+R
Sbjct: 380 CYR 382
Score = 103 bits (260), Expect = 3e-25
Identities = 34/54 (62%), Positives = 41/54 (75%)
Query: 198 VVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQQRA 251
VV++TNIAETSLTI G+ +VID G AK+K Y+PR + L PISKASA QRA
Sbjct: 316 VVLATNIAETSLTIPGIRYVIDSGLAKEKRYDPRTGLTRLETEPISKASADQRA 369
>gnl|CDD|233660 TIGR01970, DEAH_box_HrpB, ATP-dependent helicase HrpB. This model
represents HrpB, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria,
but also in a few species of other lineages. The member
from Rhizobium meliloti has been designated HelO. HrpB
is typically about 800 residues in length, while its
paralog HrpA (TIGR01967), also uncharacterized, is about
1300 amino acids long. Related characterized eukarotic
proteins are RNA helicases associated with pre-mRNA
processing [Unknown function, Enzymes of unknown
specificity].
Length = 819
Score = 151 bits (382), Expect = 1e-41
Identities = 72/191 (37%), Positives = 99/191 (51%), Gaps = 13/191 (6%)
Query: 5 ATRRQHLTRQYFDNAPLMNVPGRTHPVEIFYTPEPERDYLEAAIRTVVQIHMCEEVEGDV 64
AT +AP++ GR+ PVEI Y P LE A+ V+ H G +
Sbjct: 154 ATLDGERLSSLLPDAPVVESEGRSFPVEIRYLPLRGDQRLEDAVSRAVE-HALASETGSI 212
Query: 65 LLFLTGQEEIEEACKRIKKEIDNLGPEAGELKCIPLYSTLPPNLQQRIFEAAPANKPNGG 124
L+FL GQ EI +++ + L + + PLY L Q R + P +
Sbjct: 213 LVFLPGQAEIRRVQEQLA---ERLDSD---VLICPLYGELSLAAQDRAIKPDPQGR---- 262
Query: 125 IGRKVVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQQRAGR 184
RKVV++TNIAETSLTI+G+ VID G A+ ++P+ + L IS+ASA QRAGR
Sbjct: 263 --RKVVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETVRISQASATQRAGR 320
Query: 185 AGRTRPGKCFR 195
AGR PG C+R
Sbjct: 321 AGRLEPGVCYR 331
Score = 67.9 bits (166), Expect = 6e-13
Identities = 45/131 (34%), Positives = 66/131 (50%), Gaps = 19/131 (14%)
Query: 131 VSTNIAETSLTIDGVVFVIDPGFAK----QKVYNPRIRVESLLVSPIS---KASAQQRA- 182
VS + + G + V PG A+ Q+ R+ + L+ P+ +AQ RA
Sbjct: 197 VSRAVEHALASETGSILVFLPGQAEIRRVQEQLAERLDSDVLIC-PLYGELSLAAQDRAI 255
Query: 183 --GRAGRTRPGKCFRYIVVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVS 240
GR + VV++TNIAETSLTI+G+ VID G A+ ++P+ + L
Sbjct: 256 KPDPQGRRK--------VVLATNIAETSLTIEGIRVVIDSGLARVARFDPKTGITRLETV 307
Query: 241 PISKASAQQRA 251
IS+ASA QRA
Sbjct: 308 RISQASATQRA 318
>gnl|CDD|233659 TIGR01967, DEAH_box_HrpA, ATP-dependent helicase HrpA. This model
represents HrpA, one of two related but uncharacterized
DEAH-box ATP-dependent helicases in many Proteobacteria
and a few high-GC Gram-positive bacteria. HrpA is about
1300 amino acids long, while its paralog HrpB, also
uncharacterized, is about 800 amino acids long. Related
characterized eukarotic proteins are RNA helicases
associated with pre-mRNA processing [Unknown function,
Enzymes of unknown specificity].
Length = 1283
Score = 146 bits (369), Expect = 7e-40
Identities = 75/187 (40%), Positives = 111/187 (59%), Gaps = 22/187 (11%)
Query: 15 YFDNAPLMNVPGRTHPVEIFYTP------EPERDYLEAAIRTVVQIHMCEEVEGDVLLFL 68
+F+NAP++ V GRT+PVE+ Y P + + D LEA + V + + E GD+L+FL
Sbjct: 229 HFNNAPIIEVSGRTYPVEVRYRPLVEEQEDDDLDQLEAILDAVDE--LFAEGPGDILIFL 286
Query: 69 TGQEEIEEACKRIKKEIDNLGPEAGELKCIPLYSTLPPNLQQRIFEAAPANKPNGGIGRK 128
G+ EI +A + ++K E+ +PLY+ L QQR+F GR+
Sbjct: 287 PGEREIRDAAEILRK----RNLRHTEI--LPLYARLSNKEQQRVF--------QPHSGRR 332
Query: 129 VVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT 188
+V++TN+AETSLT+ G+ +VID G A+ Y+ R +V+ L + PIS+ASA QR GR GR
Sbjct: 333 IVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGRV 392
Query: 189 RPGKCFR 195
PG C R
Sbjct: 393 APGICIR 399
Score = 66.3 bits (162), Expect = 2e-12
Identities = 31/75 (41%), Positives = 45/75 (60%), Gaps = 7/75 (9%)
Query: 176 ASAQQRAGRAGRTRPGKCFRYIVVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVE 235
QQR + R +V++TN+AETSLT+ G+ +VID G A+ Y+ R +V+
Sbjct: 318 NKEQQRVFQPHSGRR-------IVLATNVAETSLTVPGIHYVIDTGTARISRYSYRTKVQ 370
Query: 236 SLLVSPISKASAQQR 250
L + PIS+ASA QR
Sbjct: 371 RLPIEPISQASANQR 385
>gnl|CDD|182986 PRK11131, PRK11131, ATP-dependent RNA helicase HrpA; Provisional.
Length = 1294
Score = 141 bits (358), Expect = 2e-38
Identities = 74/188 (39%), Positives = 113/188 (60%), Gaps = 22/188 (11%)
Query: 14 QYFDNAPLMNVPGRTHPVEIFYTP------EPERDYLEAAIRTVVQIHMCEEVEGDVLLF 67
++F+NAP++ V GRT+PVE+ Y P + ERD L+A V + + E GD+L+F
Sbjct: 235 RHFNNAPIIEVSGRTYPVEVRYRPIVEEADDTERDQLQAIFDAVDE--LGREGPGDILIF 292
Query: 68 LTGQEEIEEACKRIKKEIDNLGPEAGELKCIPLYSTLPPNLQQRIFEAAPANKPNGGIGR 127
++G+ EI + + K NL + +PLY+ L + Q R+F+ + G R
Sbjct: 293 MSGEREIRDTADALNKL--NLR----HTEILPLYARLSNSEQNRVFQ------SHSG--R 338
Query: 128 KVVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQQRAGRAGR 187
++V++TN+AETSLT+ G+ +VIDPG A+ Y+ R +V+ L + PIS+ASA QR GR GR
Sbjct: 339 RIVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQRKGRCGR 398
Query: 188 TRPGKCFR 195
G C R
Sbjct: 399 VSEGICIR 406
Score = 68.2 bits (167), Expect = 5e-13
Identities = 28/53 (52%), Positives = 41/53 (77%)
Query: 198 VVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQQR 250
+V++TN+AETSLT+ G+ +VIDPG A+ Y+ R +V+ L + PIS+ASA QR
Sbjct: 340 IVLATNVAETSLTVPGIKYVIDPGTARISRYSYRTKVQRLPIEPISQASANQR 392
>gnl|CDD|236950 PRK11664, PRK11664, ATP-dependent RNA helicase HrpB; Provisional.
Length = 812
Score = 128 bits (324), Expect = 7e-34
Identities = 69/191 (36%), Positives = 100/191 (52%), Gaps = 13/191 (6%)
Query: 5 ATRRQHLTRQYFDNAPLMNVPGRTHPVEIFYTPEPERDYLEAAIRTVVQIHMCEEVEGDV 64
AT +Q +AP++ GR+ PVE Y P P + A+ + + G +
Sbjct: 157 ATLDNDRLQQLLPDAPVIVSEGRSFPVERRYQPLPAHQRFDEAVARATA-ELLRQESGSL 215
Query: 65 LLFLTGQEEIEEACKRIKKEIDNLGPEAGELKCIPLYSTLPPNLQQRIFEAAPANKPNGG 124
LLFL G EI +R+++++ + L C PLY L QQ+ APA +
Sbjct: 216 LLFLPGVGEI----QRVQEQLASRVASDVLL-C-PLYGALSLAEQQKAILPAPAGR---- 265
Query: 125 IGRKVVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQQRAGR 184
RKVV++TNIAETSLTI+G+ V+D G + ++P+ + L+ IS+AS QRAGR
Sbjct: 266 --RKVVLATNIAETSLTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRAGR 323
Query: 185 AGRTRPGKCFR 195
AGR PG C
Sbjct: 324 AGRLEPGICLH 334
Score = 59.2 bits (144), Expect = 4e-10
Identities = 35/103 (33%), Positives = 53/103 (51%), Gaps = 23/103 (22%)
Query: 164 RVESLLVSPISKA------------SAQQRA---GRAGRTRPGKCFRYIVVVSTNIAETS 208
RV+ L S ++ + QQ+A AGR + VV++TNIAETS
Sbjct: 227 RVQEQLASRVASDVLLCPLYGALSLAEQQKAILPAPAGRRK--------VVLATNIAETS 278
Query: 209 LTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQQRA 251
LTI+G+ V+D G + ++P+ + L+ IS+AS QRA
Sbjct: 279 LTIEGIRLVVDSGLERVARFDPKTGLTRLVTQRISQASMTQRA 321
>gnl|CDD|197757 smart00490, HELICc, helicase superfamily c-terminal domain.
Length = 82
Score = 61.5 bits (150), Expect = 1e-12
Identities = 27/94 (28%), Positives = 37/94 (39%), Gaps = 24/94 (25%)
Query: 94 ELKCIPLYSTLPPNLQQRIFEAAPANKPNGGIGRKVVVSTNIAETSLTIDGVVFVIDPGF 153
+K L+ L ++ I + K KV+V+T++AE L + GV VI
Sbjct: 11 GIKVARLHGGLSQEEREEILDKFNNGK------IKVLVATDVAERGLDLPGVDLVIIYDL 64
Query: 154 AKQKVYNPRIRVESLLVSPISKASAQQRAGRAGR 187
P S AS QR GRAGR
Sbjct: 65 ------------------PWSPASYIQRIGRAGR 80
Score = 34.5 bits (80), Expect = 0.006
Identities = 16/57 (28%), Positives = 22/57 (38%), Gaps = 18/57 (31%)
Query: 195 RYIVVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQQRA 251
+ V+V+T++AE L + GV VI P S AS QR
Sbjct: 37 KIKVLVATDVAERGLDLPGVDLVIIYDL------------------PWSPASYIQRI 75
>gnl|CDD|238034 cd00079, HELICc, Helicase superfamily c-terminal domain; associated
with DEXDc-, DEAD-, and DEAH-box proteins, yeast
initiation factor 4A, Ski2p, and Hepatitis C virus NS3
helicases; this domain is found in a wide variety of
helicases and helicase related proteins; may not be an
autonomously folding unit, but an integral part of the
helicase; 4 helicase superfamilies at present according
to the organization of their signature motifs; all
helicases share the ability to unwind nucleic acid
duplexes with a distinct directional polarity; they
utilize the free energy from nucleoside triphosphate
hydrolysis to fuel their translocation along DNA,
unwinding the duplex in the process.
Length = 131
Score = 60.3 bits (147), Expect = 9e-12
Identities = 29/166 (17%), Positives = 56/166 (33%), Gaps = 36/166 (21%)
Query: 32 EIFYTPEPERDYLEAAIRTVVQIHMCEEVEGDVLLFLTGQEEIEEACKRIKKEIDNLGPE 91
I P D A+ +++ H + G VL+F ++ ++E + ++K
Sbjct: 1 PIKQYVLPVEDEKLEALLELLKEH--LKKGGKVLIFCPSKKMLDELAELLRK-------- 50
Query: 92 AGELKCIPLYSTLPPNLQQRIFEAAPANKPNGGIGRKVVVSTNIAETSLTIDGVVFVIDP 151
+K L+ ++ + + + V+V+T++ ID
Sbjct: 51 -PGIKVAALHGDGSQEEREEVLKDFREGEIV------VLVATDVIAR---------GIDL 94
Query: 152 GFAKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRT-RPGKCFRY 196
+ P S +S QR GRAGR + G
Sbjct: 95 PNVSVVINYDL---------PWSPSSYLQRIGRAGRAGQKGTAILL 131
>gnl|CDD|201125 pfam00271, Helicase_C, Helicase conserved C-terminal domain. The
Prosite family is restricted to DEAD/H helicases,
whereas this domain family is found in a wide variety of
helicases and helicase related proteins. It may be that
this is not an autonomously folding unit, but an
integral part of the helicase.
Length = 78
Score = 55.2 bits (134), Expect = 2e-10
Identities = 25/94 (26%), Positives = 38/94 (40%), Gaps = 24/94 (25%)
Query: 94 ELKCIPLYSTLPPNLQQRIFEAAPANKPNGGIGRKVVVSTNIAETSLTIDGVVFVIDPGF 153
+K L+ L ++ I E K KV+V+T++A + + V VI+
Sbjct: 7 GIKVARLHGGLSQEEREEILEDFRNGK------SKVLVATDVAGRGIDLPDVNLVIN--- 57
Query: 154 AKQKVYNPRIRVESLLVSPISKASAQQRAGRAGR 187
Y+ P + AS QR GRAGR
Sbjct: 58 -----YDL----------PWNPASYIQRIGRAGR 76
Score = 32.9 bits (76), Expect = 0.022
Identities = 7/25 (28%), Positives = 15/25 (60%)
Query: 195 RYIVVVSTNIAETSLTIDGVVFVID 219
+ V+V+T++A + + V VI+
Sbjct: 33 KSKVLVATDVAGRGIDLPDVNLVIN 57
>gnl|CDD|177443 PHA02653, PHA02653, RNA helicase NPH-II; Provisional.
Length = 675
Score = 45.7 bits (109), Expect = 1e-05
Identities = 47/194 (24%), Positives = 85/194 (43%), Gaps = 42/194 (21%)
Query: 13 RQYFDNAPLMNVPGRT-HPV-EIF----YTPEPERDYLEAAIRTVVQ-IHMCEEVEG-DV 64
+++F N +++PG T P+ E++ Y P+ +R Y+E + +V + +G
Sbjct: 339 KEFFPNPAFVHIPGGTLFPISEVYVKNKYNPKNKRAYIEEEKKNIVTALKKYTPPKGSSG 398
Query: 65 LLFLTGQEEIEEACKRIKKEIDNLGPEAGELKCIPLYSTLPPNLQQRIFEAAPANKPNGG 124
++F+ + EE KK ++ P ++ +P N+ + + + + P+
Sbjct: 399 IVFVASVSQCEE----YKKYLEKRLPI---YDFYIIHGKVP-NIDEILEKVYSSKNPS-- 448
Query: 125 IGRKVVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSP-------ISKAS 177
+++ST E+S+TI V D G +VY P P ISK+
Sbjct: 449 ----IIISTPYLESSVTIRNATHVYDTG----RVYVP---------EPFGGKEMFISKSM 491
Query: 178 AQQRAGRAGRTRPG 191
QR GR GR PG
Sbjct: 492 RTQRKGRVGRVSPG 505
Score = 30.3 bits (69), Expect = 0.91
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 4/34 (11%)
Query: 198 VVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPR 231
+++ST E+S+TI V D G +VY P
Sbjct: 449 IIISTPYLESSVTIRNATHVYDTG----RVYVPE 478
Score = 27.2 bits (61), Expect = 9.9
Identities = 18/44 (40%), Positives = 26/44 (59%), Gaps = 10/44 (22%)
Query: 98 IPLYSTLPPNLQQRIFEAAPANKPNGGIGRKVVVS--TNIAETS 139
IPL S L P++Q +IFEA + KP VV++ T + +TS
Sbjct: 159 IPLAS-LQPDVQLKIFEAWISRKP-------VVLTGGTGVGKTS 194
>gnl|CDD|173301 PRK14840, PRK14840, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 250
Score = 33.3 bits (76), Expect = 0.088
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 6/72 (8%)
Query: 67 FLTGQEEIEEACKRIKKEIDNLGPEAGE----LKCIPLYSTLPPNLQQRIFEAAPANKPN 122
F +EE+ E ++D+ P E L+CI S LP LQ I +A+ A
Sbjct: 80 FSRSKEEVAELFSLFNSQLDSQLPYLHENEIRLRCIGDLSKLPQELQNNIEQASSATAHY 139
Query: 123 GGIGRKVVVSTN 134
++V++ N
Sbjct: 140 S--RMELVLAIN 149
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 30.8 bits (70), Expect = 0.79
Identities = 21/65 (32%), Positives = 28/65 (43%), Gaps = 18/65 (27%)
Query: 128 KVVVSTNIAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQQRAGRAGR 187
V+V+T++ E L I V VI Y P + S I + QR GR GR
Sbjct: 427 NVLVATSVGEEGLDIPEVDLVI--------FYEP-------VPSEIR---SIQRKGRTGR 468
Query: 188 TRPGK 192
R G+
Sbjct: 469 KRKGR 473
>gnl|CDD|184841 PRK14831, PRK14831, undecaprenyl pyrophosphate synthase;
Provisional.
Length = 249
Score = 29.5 bits (67), Expect = 1.2
Identities = 21/77 (27%), Positives = 34/77 (44%), Gaps = 12/77 (15%)
Query: 58 EEVEGDVLLFLTGQEEIEEACKRIKKEIDNLGPEAGELKCIPLYSTLPPNLQQRIFEAAP 117
EEV + LF E + +++E++ L E ++ + LP +LQ+ I +
Sbjct: 83 EEVNFLMTLF----ERV------LRRELEELMEENVRIRFVGDLDPLPKSLQEEISRSTE 132
Query: 118 ANKPNGGIGRKVVVSTN 134
K N GI V TN
Sbjct: 133 LTKNNNGI--HFNVCTN 147
>gnl|CDD|149487 pfam08440, Poty_PP, Potyviridae polyprotein. This domain is found
in polyproteins of the viral Potyviridae taxon.
Length = 274
Score = 29.1 bits (66), Expect = 2.1
Identities = 14/46 (30%), Positives = 25/46 (54%), Gaps = 3/46 (6%)
Query: 98 IPLY-STLPPNLQQRIFEAAPANKPNGGIGRKVVVSTNIAETSLTI 142
IP Y +P L ++++EA KP+ G GR + S + + + T+
Sbjct: 107 IPFYVKDVPDKLYEKLWEAVLKYKPDAGFGR--LSSASACKIAYTL 150
>gnl|CDD|184755 PRK14583, hmsR, N-glycosyltransferase; Provisional.
Length = 444
Score = 28.8 bits (64), Expect = 2.7
Identities = 41/162 (25%), Positives = 63/162 (38%), Gaps = 33/162 (20%)
Query: 91 EAGELKCIPLYSTLPP------NLQQRIFEAAPANKPNGGIGRKVVVSTNIAETSLTIDG 144
A ELK PL S L P N ++ I A N V++ N + T
Sbjct: 67 PAPELKGHPLVSILVPCFNEGLNARETIHAALAQTYTN-----IEVIAINDGSSDDTAQ- 120
Query: 145 VVFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTRPGKCFRYIVVVSTNI 204
V+D + +PR+RV L + KA A + A R+ Y+V +
Sbjct: 121 ---VLD-ALLAE---DPRLRVIHLAHNQ-GKAIALRMGAAAARSE------YLVCID--- 163
Query: 205 AETSLTIDGVVFVIDPGFAKQKVY----NPRIRVESLLVSPI 242
+ L + V +++ P A + NPRIR S L+ +
Sbjct: 164 GDALLDKNAVPYLVAPLIANPRTGAVTGNPRIRTRSTLIGRV 205
>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
domain including a metal-binding cysteine cluster
[General function prediction only].
Length = 851
Score = 28.9 bits (65), Expect = 3.3
Identities = 12/28 (42%), Positives = 17/28 (60%), Gaps = 1/28 (3%)
Query: 172 PISKASAQQRAGRAGRTRPGKCFRYIVV 199
+S S +QRAGRAGR R + +V+
Sbjct: 393 GVSVLSFRQRAGRAGR-RGQESLVLVVL 419
>gnl|CDD|132218 TIGR03174, cas_Csc3, CRISPR type I-D/CYANO-associated protein
Csc3/Cas10d. CRISPR (Clustered Regularly Interspaced
Short Palindromic Repeats) is a widespread family of
prokaryotic direct repeats with spacers of unique
sequence between consecutive repeats. This protein
family is a CRISPR-associated (Cas) family strictly
associated with the Cyano subtype of CRISPR/Cas locus,
found in several species of Cyanobacteria and several
archaeal species. This family is designated Csc3 for
CRISPR/Cas Subtype Cyano protein 3, as it is often the
third gene upstream of the core cas genes,
cas3-cas4-cas1-cas2 [Mobile and extrachromosomal element
functions, Other].
Length = 953
Score = 28.3 bits (63), Expect = 4.4
Identities = 19/76 (25%), Positives = 28/76 (36%), Gaps = 15/76 (19%)
Query: 126 GRKVVVSTNIA---------ETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKA 176
G KVV S + S+ +DG P F R+R+E + ++K
Sbjct: 684 GVKVVASESPIPLMRSGQEFRESVHLDGA-----PHFWVLLGIPDRLRLED-ITPALNKL 737
Query: 177 SAQQRAGRAGRTRPGK 192
A A R+ P K
Sbjct: 738 LAIYTLHLAIRSSPPK 753
>gnl|CDD|223630 COG0556, UvrB, Helicase subunit of the DNA excision repair complex
[DNA replication, recombination, and repair].
Length = 663
Score = 28.3 bits (64), Expect = 4.4
Identities = 18/74 (24%), Positives = 33/74 (44%), Gaps = 23/74 (31%)
Query: 31 VEIFYTPEPERDYLEAAIR------TVVQIHMCEEVEGDVL------------LFLTGQE 72
VEIF Y + AIR + +I + + G V+ ++T +E
Sbjct: 200 VEIFPA-----YYDDEAIRIEFFGDEIERISEFDPLTGQVIGELDRFTIYPASHYVTPRE 254
Query: 73 EIEEACKRIKKEID 86
+E+A + IK+E++
Sbjct: 255 RLEQAIESIKEELE 268
>gnl|CDD|233063 TIGR00631, uvrb, excinuclease ABC, B subunit. All proteins in this
family for wich functions are known are DNA helicases
that function in the nucleotide excision repair and are
endonucleases that make the 3' incision next to DNA
damage. They are part of a pathway requiring UvrA, UvrB,
UvrC, and UvrD homologs. 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 = 655
Score = 28.4 bits (64), Expect = 4.4
Identities = 20/74 (27%), Positives = 35/74 (47%), Gaps = 23/74 (31%)
Query: 31 VEIFYTPEPERDYLEAAIR------TVVQIHMCEEVEGDVL------------LFLTGQE 72
VEIF P E ++ A+R + +I + + G+VL ++T +E
Sbjct: 197 VEIF--PAYEDEF---AVRIEFFGDEIERISRVDPLTGEVLRELDSFTIFPASHYVTPEE 251
Query: 73 EIEEACKRIKKEID 86
+E A K I+KE++
Sbjct: 252 RLERAIKNIEKELE 265
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 28.5 bits (64), Expect = 4.5
Identities = 13/51 (25%), Positives = 21/51 (41%), Gaps = 1/51 (1%)
Query: 40 ERDYLEAAIRTVVQIHMCEEVEGDVLLFLTGQEEIEEACKRIKKEIDNLGP 90
D L+ + + + EE E +EE KR++ +I LGP
Sbjct: 937 RIDNLQERLSEEYSLTL-EEAEALENKIEDDEEEARRRLKRLENKIKELGP 986
>gnl|CDD|201832 pfam01507, PAPS_reduct, Phosphoadenosine phosphosulfate reductase
family. This domain is found in phosphoadenosine
phosphosulfate (PAPS) reductase enzymes or PAPS
sulfotransferase. PAPS reductase is part of the adenine
nucleotide alpha hydrolases superfamily also including
N type ATP PPases and ATP sulphurylases. The enzyme
uses thioredoxin as an electron donor for the reduction
of PAPS to phospho-adenosine-phosphate (PAP). It is
also found in NodP nodulation protein P from Rhizobium
which has ATP sulfurylase activity (sulfate adenylate
transferase).
Length = 173
Score = 27.6 bits (62), Expect = 4.9
Identities = 13/75 (17%), Positives = 29/75 (38%), Gaps = 6/75 (8%)
Query: 10 HLTRQYFDNAPLMNV-PGRTHPVEIFYTPEPERDYLEAAIRTVVQIHMCEEVEGDVLLFL 68
HL + F P++ + G P + D LE +++++ E+ + +
Sbjct: 17 HLASKAFPPGPVIFIDTGYEFPETYEF-----VDELEEKYGLNLKVYLPEDSFAEGINPE 71
Query: 69 TGQEEIEEACKRIKK 83
+ C R++K
Sbjct: 72 GIPSSLYRRCCRLRK 86
>gnl|CDD|235596 PRK05764, PRK05764, aspartate aminotransferase; Provisional.
Length = 393
Score = 27.8 bits (63), Expect = 5.5
Identities = 7/20 (35%), Positives = 15/20 (75%)
Query: 69 TGQEEIEEACKRIKKEIDNL 88
T E++EE +RI++ +++L
Sbjct: 373 TSLEDLEEGLERIERFLESL 392
>gnl|CDD|198397 cd10450, GIY-YIG_AtGrxS16_like, GIY-YIG domain found in
CAXIP1-like proteins, iron-sulfur cluster assembly
proteins, and similar proteins. The family includes
CAX-interacting protein-1 (CXIP1)-like proteins and
iron-sulfur cluster assembly proteins, both of which
contain a GIY-YIG domain that shows statistically
significant similarity to the N-terminal catalytic
domains of GIY-YIG family of intron-encoded homing
endonuclease I-TevI and catalytic GIY-YIG domain of
nucleotide excision repair endonuclease UvrC. CAXIP1 is
a novel PICOT (protein kinase C-interacting cousin of
thioredoxin) domain-containing Arabidopsis protein that
activates H+/Ca2+ exchanger CAX1, and its homolog CAX4,
but not CAX2 or CAX3. Iron-sulfur cluster assembly
proteins in this family also contain a C-terminal
NifU-like domain that corresponds to a common region
between the NifU protein from nitrogen-fixing bacteria
and rhodobacterial species. The biochemical function of
NifU is unknown.
Length = 70
Score = 25.7 bits (57), Expect = 5.8
Identities = 12/40 (30%), Positives = 15/40 (37%), Gaps = 10/40 (25%)
Query: 8 RQHLTRQYFDNAPLMNVPGRTHPVEIFYTPEPERDYLEAA 47
R HL R P H V++ P+R LEA
Sbjct: 26 RTHLARV----------PELCHSVKVAIFDRPDRAALEAV 55
>gnl|CDD|235395 PRK05298, PRK05298, excinuclease ABC subunit B; Provisional.
Length = 652
Score = 27.7 bits (63), Expect = 7.2
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 23/72 (31%)
Query: 31 VEIFYTPEPERDYLEAAIR------TVVQIHMCEEVEGDVL------------LFLTGQE 72
+EIF P Y E AIR + +I + + G+VL ++T +E
Sbjct: 200 IEIF----P-AYYEERAIRIEFFGDEIERISEFDPLTGEVLGELDRVTIYPASHYVTPRE 254
Query: 73 EIEEACKRIKKE 84
+E A + IK+E
Sbjct: 255 RLERAIESIKEE 266
>gnl|CDD|153118 cd07909, YciF, YciF bacterial stress response protein,
ferritin-like iron-binding domain. YciF is a bacterial
protein of unknown function that is up-regulated when
bacteria experience stress conditions, and is highly
conserved in a broad range of bacterial species. YciF
has a ferritin-like domain. Ferritin-like,
diiron-carboxylate proteins participate in a range of
functions including iron regulation, mono-oxygenation,
and reactive radical production. These proteins are
characterized by the fact that they catalyze
dioxygen-dependent oxidation-hydroxylation reactions
within diiron centers; one exception is manganese
catalase, which catalyzes peroxide-dependent
oxidation-reduction within a dimanganese center.
Diiron-carboxylate proteins are further characterized
by the presence of duplicate metal ligands, glutamates
and histidines (ExxH) and two additional glutamates
within a four-helix bundle. Outside of these conserved
residues there is little obvious homology. Members
include bacterioferritin, ferritin, rubrerythrin,
aromatic and alkene monooxygenase hydroxylases (AAMH),
ribonucleotide reductase R2 (RNRR2),
acyl-ACP-desaturases (Acyl_ACP_Desat), manganese (Mn)
catalases, demethoxyubiquinone hydroxylases (DMQH), DNA
protecting proteins (DPS), and ubiquinol oxidases
(AOX), and the aerobic cyclase system, Fe-containing
subunit (ACSF).
Length = 147
Score = 26.8 bits (60), Expect = 7.6
Identities = 11/44 (25%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 56 MCEEVEGDVL--LFLTGQEEIEEACKRIKKEIDNLGPEAGELKC 97
M + + L F + EE E +R+++ ++LG + KC
Sbjct: 25 MAKAATSEELKEAFESHLEETEGQVERLEQIFESLGEKPEGKKC 68
>gnl|CDD|233184 TIGR00917, 2A060601, Niemann-Pick C type protein family. The model
describes Niemann-Pick C type protein in eukaryotes. The
defective protein has been associated with Niemann-Pick
disease which is described in humans as autosomal
recessive lipidosis. It is characterized by the
lysosomal accumulation of unestrified cholesterol. It is
an integral membrane protein, which indicates that this
protein is most likely involved in cholesterol transport
or acts as some component of cholesterol homeostasis
[Transport and binding proteins, Other].
Length = 1204
Score = 27.5 bits (61), Expect = 7.9
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 196 YIVVVSTNIAETSLTIDGVVFVIDPGFAKQKVYN 229
++ V ST +T+ T+D V + I FA +YN
Sbjct: 97 FMNVTSTTKVKTNSTVDSVQYYITDDFA-NGMYN 129
>gnl|CDD|237496 PRK13766, PRK13766, Hef nuclease; Provisional.
Length = 773
Score = 27.5 bits (62), Expect = 8.0
Identities = 22/73 (30%), Positives = 28/73 (38%), Gaps = 30/73 (41%)
Query: 128 KVVVSTNIAETSLTI---DGVVFVIDPGFAKQKVYNP---RIRVESLLVSPISKASAQQR 181
V+VST++AE L I D V+F Y P IR + QR
Sbjct: 425 NVLVSTSVAEEGLDIPSVDLVIF-----------YEPVPSEIR-------------SIQR 460
Query: 182 AGRAGRTRPGKCF 194
GR GR G+
Sbjct: 461 KGRTGRQEEGRVV 473
>gnl|CDD|131967 TIGR02921, PEP_integral, PEP-CTERM family integral membrane
protein. Members of this protein family, found in three
different species so far, have a PEP-CTERM sequence at
the carboxyl-terminus (see model TIGR02595), but are
unusual among PEP-CTERM proteins in having multiple
predicted transmembrane segments. The function is
unknown. It is proposed that a member of the EpsH
family, to be designated exosortase (see TIGR02602),
recognizes and cleaves PEP-CTERM proteins in a manner
analogous to the cleavage of LPXTG proteins by sortase
(see Haft, et al., 2006).
Length = 952
Score = 27.3 bits (60), Expect = 8.7
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 135 IAETSLTIDGVVFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQQRAGRAGRTR 189
+ + + D F + P A QKVYN ++ E PI A +Q R R R
Sbjct: 465 LGDDAKDDDKFAFALAPRGAAQKVYNDEVQQE----RPIDPALLEQVGPRHYRLR 515
>gnl|CDD|226583 COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA
uptake (late competence protein) [DNA replication,
recombination, and repair].
Length = 441
Score = 27.4 bits (61), Expect = 8.9
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 20/66 (30%)
Query: 128 KVVVSTNIAETSLTIDGV-VFVIDPGFAKQKVYNPRIRVESLLVSPISKASAQQRAGRAG 186
++++T I E +T V VFV+ A+ +V+ ++++ Q AGR G
Sbjct: 357 TLLITTTILERGVTFPNVDVFVLG---AEHRVF--------------TESALVQIAGRVG 399
Query: 187 R--TRP 190
R RP
Sbjct: 400 RSLERP 405
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
0.319 0.136 0.391
Gapped
Lambda K H
0.267 0.0781 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,160,573
Number of extensions: 1274127
Number of successful extensions: 1566
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1540
Number of HSP's successfully gapped: 56
Length of query: 251
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 156
Effective length of database: 6,723,972
Effective search space: 1048939632
Effective search space used: 1048939632
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.0 bits)