RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780882|ref|YP_003065295.1| site-specific tyrosine
recombinase XerC [Candidatus Liberibacter asiaticus str. psy62]
(328 letters)
>gnl|CDD|29499 cd00798, INT_XerDC, XerD and XerC integrases, DNA
breaking-rejoining enzymes, N- and C-terminal domains.
XerD-like integrases are involved in the site-specific
integration and excision of lysogenic bacteriophage
genomes, transposition of conjugative transposons,
termination of chromosomal replication, and stable
plasmid inheritance. They share the same fold in their
catalytic domain containing six conserved active site
residues and the overall reaction mechanism with the DNA
breaking-rejoining enzyme superfamily. In Escherichia
coli, the Xer site-specific recombination system acts to
convert dimeric chromosomes, which are formed by
homologous recombination to monomers. Two related
recombinases, XerC and XerD, bind cooperatively to a
recombination site present in the E. coli chromosome.
Each recombinase catalyzes the exchange of one pair of
DNA strand in a reaction that proceeds through a
Holliday junction intermediate. These enzymes can bridge
two different and well-separated DNA sequences called
arm- and core-sites. The C-terminal domain binds,
cleaves and re-ligates DNA strands at the core-sites,
while the N-terminal domain is largely responsible for
high-affinity binding to the arm-type sites..
Length = 284
Score = 217 bits (554), Expect = 3e-57
Identities = 100/285 (35%), Positives = 157/285 (55%), Gaps = 11/285 (3%)
Query: 19 QNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKR 78
+ +L L +ERGLS+ TL +Y D +FL FL E+ I ++ +IR F+++
Sbjct: 2 ERFLDYLAVERGLSENTLAAYRRDLERFLEFL-----EERGILFPADVTPDDIRRFLAEL 56
Query: 79 RTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLV 138
+ Q + RS+ R LS ++SF K+L + + + + K SLP+ L ++ L+
Sbjct: 57 KDQGLSARSIARKLSALRSFFKFLLREGLILANPAELIEPPKLKRSLPKVLTIEEVERLL 116
Query: 139 DNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIR 198
T R+ A+L LLY GLR+SE + L ++ + +R++GKG+K R
Sbjct: 117 AAPDGDTPLG-----LRDRALLELLYSTGLRVSELVGLKLSDVDLSRGLIRVRGKGNKER 171
Query: 199 IVPLLPSVRKAILEYYDLC-PFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLP 257
IVPL + +A+ Y ++ P L + LF RGK L+ + +++ R G+
Sbjct: 172 IVPLGETAVEALQRYLEVRRPLLLKVGDSDALFLNQRGKRLSRRGVWKILKEYARRAGIE 231
Query: 258 LSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVN 302
+ HTLRHSFATHLL NG DLR++Q +LGH L+TTQIYT+V+
Sbjct: 232 KKISPHTLRHSFATHLLENGADLRAVQELLGHASLATTQIYTHVS 276
>gnl|CDD|34580 COG4974, XerD, Site-specific recombinase XerD [DNA replication,
recombination, and repair].
Length = 300
Score = 201 bits (512), Expect = 3e-52
Identities = 101/303 (33%), Positives = 158/303 (52%), Gaps = 16/303 (5%)
Query: 19 QNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKR 78
+ +L+ L IERGLS TL SY D F +L E+ I + + +IR ++++
Sbjct: 10 EQFLEYLWIERGLSANTLSSYRRDLEDFREWL-----EERGITDLADATEADIREYLTEL 64
Query: 79 RTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLV 138
Q + S+ R+LS ++SF ++L + + + + + K LP+ L+E++
Sbjct: 65 AEQGLSATSIARALSALRSFYQFLIREGLREDDPTRLLDSPKLPKRLPKFLSEEEV---- 120
Query: 139 DNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIR 198
LL E + R+ A+L LLY GLR+SE + LT ++ Q +R++GKG+K R
Sbjct: 121 -EALLEAPDEDTPLGLRDRAMLELLYATGLRVSELVGLTLSDVDLRQGVVRVRGKGNKER 179
Query: 199 IVPLLPSVRKAILEYY-DLCPFDLNLNIQLP-LFRGIRGKPLNPGVFQRYIRQLRRYLGL 256
+VP +A+ +Y + P L LF RG L F + ++ G+
Sbjct: 180 LVPFGEEAVEALEKYLEEARPKLLKGKSSTDALFPNQRGGGLTRQGFWKRLKDYAERAGI 239
Query: 257 PLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQ 316
+ HTLRHSFATHLL NG DLR +Q +LGH +STTQIYT+V + + ++Y Q
Sbjct: 240 DKKISPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVTK----ERLRDLYAQ 295
Query: 317 THP 319
HP
Sbjct: 296 HHP 298
>gnl|CDD|34579 COG4973, XerC, Site-specific recombinase XerC [DNA replication,
recombination, and repair].
Length = 299
Score = 167 bits (425), Expect = 3e-42
Identities = 97/304 (31%), Positives = 158/304 (51%), Gaps = 17/304 (5%)
Query: 21 WLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRT 80
+L+ L +ER LS TL +Y RQ +A ++ + + +QL ++RAF+++
Sbjct: 13 YLRYLRVERQLSPHTLANYR---RQLEALIALL--AQMGLGSWQQLDPADVRAFVARSHR 67
Query: 81 QKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDN 140
+ + RSL R LS ++SF +L K+ + + K+ LP+ L+ +A L+D
Sbjct: 68 RGLSARSLARRLSALRSFYDWLVKQGELKANPAKGVSAPKQPRHLPKNLDVDEANRLLDI 127
Query: 141 VLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIV 200
+ R+ A+L L+YG GLR+SE + L +++ D+ +R+ GKG+K R V
Sbjct: 128 D------GDDPLAVRDRALLELMYGSGLRLSELVGLDLKHVDLDEGEVRVMGKGNKERRV 181
Query: 201 PLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLST 260
P+ +A+ + L L + LF GK ++ Q+ + Q GL
Sbjct: 182 PVGRKAVEALEHWLALRG--LFASEDDALFLSRLGKRISARAIQKRLAQWGIKQGLNSHV 239
Query: 261 TAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPS 320
H LRHSFATH+L + GDLR++Q +LGH LSTTQIYT+++ + +YD HP
Sbjct: 240 HPHKLRHSFATHMLESSGDLRAVQELLGHANLSTTQIYTHLDF----QHLASVYDAAHPR 295
Query: 321 ITQK 324
+K
Sbjct: 296 AKRK 299
>gnl|CDD|29514 cd01193, INT_IntI, IntI (E2) integrases, site-specific tyrosine
recombinases, DNA breaking-rejoining enzymes, N- and
C-terminal domains. This CD includes integrases which
are components of multiresistant integrons and mediate
recombination between a proximal attI site and a
secondary target called the attC (or 59-base element)
present on various mobile gene cassettes.
Integron-integrases are present in many natural
occurring mobile elements, including transposons and
conjugative plasmids. Vibrio, Shewanella, Xanthomonas
and Pseudomonas species harbor chromosomal
super-integrons. All integron-integrases carry large
inserts unlike the TnpF ermF-like proteins also seen in
this group..
Length = 242
Score = 134 bits (338), Expect = 4e-32
Identities = 78/248 (31%), Positives = 118/248 (47%), Gaps = 23/248 (9%)
Query: 64 RQLSYTEIRAFISKRRTQ-KIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKS 122
+L ++RAF++ + + + ++LS + F ++ KR + I R +K
Sbjct: 8 DELGEEDVRAFLTLLAVEGNVSASTQNQALSALLFFYRHTLKRDLPWLQRI---RRPRKP 64
Query: 123 NSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIM 182
LP L+ ++ V +L + IL LLYGCGLR+SE L L ++I
Sbjct: 65 RKLPVVLSPEE----VRRLLGALTGLKHR------LILSLLYGCGLRLSECLRLRVKDID 114
Query: 183 DDQSTLRI-QGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRG--------I 233
D+ +R+ QGKG K R V L ++ + + Y+ LF
Sbjct: 115 FDRGQIRVRQGKGGKDRYVMLPEALLELLRAYWKRARALGRERPWQWLFPSTRRSRDPVE 174
Query: 234 RGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLS 293
R L+ QR +++ G+ T HTLRHSFATHLL G D+R+IQ +LGH L
Sbjct: 175 RRHHLSERTLQRALKKAVEQAGIDKRVTPHTLRHSFATHLLEAGYDIRTIQELLGHSDLK 234
Query: 294 TTQIYTNV 301
TT IYT+V
Sbjct: 235 TTMIYTHV 242
>gnl|CDD|144254 pfam00589, Phage_integrase, Phage integrase family. Members of
this family cleave DNA substrates by a series of
staggered cuts, during which the protein becomes
covalently linked to the DNA through a catalytic
tyrosine residue at the carboxy end of the alignment.
The catalytic site residues in CRE recombinase are
Arg-173, His-289, Arg-292 and Tyr-324.
Length = 170
Score = 132 bits (334), Expect = 1e-31
Identities = 65/177 (36%), Positives = 87/177 (49%), Gaps = 11/177 (6%)
Query: 127 RALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQS 186
R L E + L+ + ++ R+ A++ LL GLRISE LSL +I D
Sbjct: 1 RRLTEDEVERLLAALEEP-------LNIRDRALVELLLLTGLRISELLSLRWSDIDLDNG 53
Query: 187 TLRI-QGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQR 245
T+RI Q K K R VPL + +A+ E+ LF RGKPL+ R
Sbjct: 54 TIRIPQTKTRKSRTVPLSDAALEALKEWLGDRKEAEESEF---LFVSRRGKPLSRSTVNR 110
Query: 246 YIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVN 302
R+ + G+ T H LRH+FATHL NG LR IQ +LGH +S T YT+V
Sbjct: 111 AFRRAGKRAGIEKDLTPHDLRHTFATHLAENGVPLRVIQKLLGHSSISMTMRYTHVA 167
>gnl|CDD|29503 cd01182, INT_REC_C, DNA breaking-rejoining enzymes,
intergrase/recombinases, C-terminal catalytic domain.
The tyrosine recombinase/integrase family share the same
catalytic domain containing six conserved active site
residues. The best-studied members of this diverse
family include the bacteriophage lambda integrase, the
bacteriophage P1 Cre recombinase, the yeast Flp
recombinase and the bacterial XerD/C recombinases. Their
overall reaction mechanism is essentially identical and
involves cleavage of a single strand of a DNA duplex by
nucleophilic attack of a conserved tyrosine to give a 3'
phosphotyrosyl protein-DNA adduct. In the second
rejoining step, a terminal 5' hydroxyl attacks the
covalent adduct to release the enzyme and generate
duplex DNA. Many intergrase/recombinases also have
N-terminal domains, which show little sequence or
structure similarity..
Length = 162
Score = 109 bits (274), Expect = 8e-25
Identities = 52/149 (34%), Positives = 77/149 (51%), Gaps = 1/149 (0%)
Query: 152 IDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRI-QGKGDKIRIVPLLPSVRKAI 210
R+ A++ LL GLR+SE L+L +I D+ T+ + + K K R VPL P + + +
Sbjct: 13 TAPRDRALILLLLYTGLRVSELLALRWSDIDLDKGTITVRRTKTGKERTVPLSPELAELL 72
Query: 211 LEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFA 270
EY +L + L R K L +R +++ + G+P T H LRH+FA
Sbjct: 73 REYLELRRPAPKPDDYLFPSRRGGPKRLTRRAVRRLLKKAGKRAGIPERLTPHDLRHTFA 132
Query: 271 THLLSNGGDLRSIQSILGHFRLSTTQIYT 299
T LL G L IQ +LGH +STT+ Y
Sbjct: 133 TRLLEAGVPLEVIQELLGHSSISTTERYL 161
>gnl|CDD|29511 cd01190, INT_SG5, INT_SG5, DNA breaking-rejoining enzymes,
integrase/recombinases subgroup 5, N- and C-terminal
domains. The CD contains mainly predicted bacterial
integrase/recombinases..
Length = 260
Score = 101 bits (253), Expect = 3e-22
Identities = 71/255 (27%), Positives = 102/255 (40%), Gaps = 25/255 (9%)
Query: 62 TIRQLSYTEIRAF---ISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRN 118
I + I AF + R I R+ + L+ + SF +Y + I +
Sbjct: 4 EIEDIDAPLILAFLDHLENDRGNSIRTRNAR--LAALHSFFRYAAREVPEHLPTIQRVLA 61
Query: 119 LKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTP 178
+ R L V LL W R+ A+L LY G R+SEA L
Sbjct: 62 IP-MKRFKRPLVTYLTREEVQ-ALLAAPDRRTWSGRRDRAMLLFLYNTGARVSEATGLKV 119
Query: 179 QNI-MDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKP 237
++ +D + +R+ GKG K R VPL S A+ + PLF RG+P
Sbjct: 120 DDLQLDPPAQVRLIGKGRKERTVPLWRSTAAALRAWLRERG---LHAEDEPLFVNRRGEP 176
Query: 238 LN-PGVFQRYIRQLRRYLGLPLST---------TAHTLRHSFATHLLSNGGDLRSIQSIL 287
+ GV LR++ +T + H LRH+ A HLL +G D+ I L
Sbjct: 177 MTRFGVTYL----LRKHAAKAAATAPTLATKRISPHVLRHTTAMHLLQSGVDIVVIALWL 232
Query: 288 GHFRLSTTQIYTNVN 302
GH L TT IY +
Sbjct: 233 GHASLETTNIYAEAD 247
>gnl|CDD|29495 cd00397, DNA_BRE_C, DNA breaking-rejoining enzymes, C-terminal
catalytic domain. The DNA breaking-rejoining enzyme
superfamily includes type IB topoisomerases and tyrosine
recombinases that share the same fold in their catalytic
domain containing six conserved active site residues.
The best-studied members of this diverse superfamily
include human topoisomerase I, the bacteriophage lambda
integrase, the bacteriophage P1 Cre recombinase, the
yeast Flp recombinase and the bacterial XerD/C
recombinases. Their overall reaction mechanism is
essentially identical and involves cleavage of a single
strand of a DNA duplex by nucleophilic attack of a
conserved tyrosine to give a 3' phosphotyrosyl
protein-DNA adduct. In the second rejoining step, a
terminal 5' hydroxyl attacks the covalent adduct to
release the enzyme and generate duplex DNA. The enzymes
differ in that topoisomerases cleave and then rejoin the
same 5' and 3' termini, whereas a site-specific
recombinase transfers a 5' hydroxyl generated by
recombinase cleavage to a new 3' phosphate partner
located in a different duplex region. Many DNA
breaking-rejoining enzymes also have N-terminal domains,
which show little sequence or structure similarity..
Length = 164
Score = 96.6 bits (240), Expect = 7e-21
Identities = 50/148 (33%), Positives = 68/148 (45%), Gaps = 3/148 (2%)
Query: 155 RNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQG-KGDKIRIVPLLPSVRKAILEY 213
R L LL GLRISE +L +I D+ + I G K K R VPL K + EY
Sbjct: 16 RLYLALLLLLATGLRISELCALRWSDIDLDKRVIHITGTKTKKERTVPLSEEALKLLKEY 75
Query: 214 YDLCPFDLNLNIQL-PLFRGIRGKPLNPGVFQRYIRQLRRYLGL-PLSTTAHTLRHSFAT 271
L P RG L+ +R + R G+ T H+LRH+FA+
Sbjct: 76 LKKRRPANGDEEYLFPSRRGGPAATLSRRNVKRIFKAAGRRAGIDKEGLTPHSLRHTFAS 135
Query: 272 HLLSNGGDLRSIQSILGHFRLSTTQIYT 299
LL+ G DL ++Q +LGH ++ T Y
Sbjct: 136 ALLNAGLDLEAVQDLLGHSSIAMTMRYA 163
>gnl|CDD|29509 cd01188, INT_pAE1, pAE1 and related integrases, DNA
breaking-rejoining enzymes, integrase/recombinases,
C-terminal domain. This CD includes various bacterial
integrases, including the predicted integrase of the
deletion-prone region of plasmid pAE1 of Alcaligenes
eutrophus H1..
Length = 188
Score = 79.9 bits (197), Expect = 8e-16
Identities = 58/184 (31%), Positives = 81/184 (44%), Gaps = 17/184 (9%)
Query: 125 LPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDD 184
LPRAL + L+ + T + R+ AIL LL GLR E +L +I
Sbjct: 1 LPRALPWEDVERLLASCDRSTP-----VGRRDYAILLLLARLGLRAGEVAALRLDDIDWR 55
Query: 185 QSTLRI-QGKGDKIRIVPLLPSVRKAILEYYDL----CPFD-LNLNIQLPLFRGIRGKPL 238
T+R+ QGKG ++ +PL V A+ +Y + L ++ P FR G
Sbjct: 56 TGTIRVRQGKGGRVTRLPLPAEVGAALADYLRDGRPATDSRRVFLRMRAP-FRPFAG--- 111
Query: 239 NPGVFQRYIRQLRRYLGLPLSTT-AHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQI 297
+R+ R G+ AH LRHS AT LL G L+ I +LGH +T I
Sbjct: 112 -HSAVSNIVRRALRRAGISPRRGGAHLLRHSLATRLLRAGAPLKEIGDVLGHRSPDSTAI 170
Query: 298 YTNV 301
Y V
Sbjct: 171 YAKV 174
>gnl|CDD|29506 cd01185, INT_Tn4399, Tn4399 and related integrases, DNA
breaking-rejoining enzymes, integrase/recombinases, N-
and C-terminal domains. This CD includes various
bacterial integrases, including cLV25, a Bacteroides
fragilis chromosomal transfer factor integrase similar
to the Bacteroides mobilizable transposon, Tn4399,
integrase..
Length = 299
Score = 78.0 bits (192), Expect = 3e-15
Identities = 60/285 (21%), Positives = 109/285 (38%), Gaps = 27/285 (9%)
Query: 24 NLEIERGLSKLTLQSYECDTRQFLIFLAF--YTEEKITIQTIRQLSYTEIRAF-ISKRRT 80
N E ER +++ F T ++I I + +L+ I F + R+
Sbjct: 23 NDERERVGKDKAQSTWKRYRTHLKNLREFIECTYKEIDI-ALLELTREFILEFKLFLRKE 81
Query: 81 QKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALTLVDN 140
+K+ + LS +K LK + K ++ + K+ + L + L +
Sbjct: 82 KKLSRNTAVHYLSWLKKLLKIAYRDKGLRDNPFAKFKCKKEEETDREYLTPDELQKLAET 141
Query: 141 VLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLR----IQGKGDK 196
E R + + GLR S+ LT + I++D + + K
Sbjct: 142 PCKDPRLE----LVRRAFLFSCF--TGLRYSDIKKLTWEEIVEDSDGEKWIRKRRQKTKV 195
Query: 197 IRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGL 256
+PLL IL Y +F ++ +N + +++ + G+
Sbjct: 196 EVYIPLLD-EALQILGKYP--DEKEG-----LVFPLLKNSNMN-----KPLKEWAKLAGI 242
Query: 257 PLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNV 301
T H RH+FAT L +GG + ++ +LGH + TTQ+Y V
Sbjct: 243 KKHITFHCARHTFATLQLLSGGPIETVSKMLGHTNIKTTQVYARV 287
>gnl|CDD|29498 cd00797, HP1_INT_C, Phage HP1 integrase, C-terminal catalytic
domain. Bacteriophage HP1 and related integrases are
found in eubacteria, plasmids and temperate
bacteriophages of the P2 family. They belong to the DNA
breaking-rejoining enzyme superfamily, which includes
tyrosine recombinases and type IB topoisomerases. These
enzymes share the same fold in their C-terminal
catalytic domain containing six conserved active site
residues and the overall reaction mechanism. The HP1
recombinase controls phage replication by site-specific
recombination between the HP1 genome and the chromosomal
DNA. It is a heterobifunctional DNA-binding protein,
which recognizes two different DNA sequence motifs (type
I and type II binding sites). The C-terminal catalytic
domain of the HP1 integrase binds to the type I site,
while the less conserved N-terminal domain is largely
responsible for binding to the type II site..
Length = 158
Score = 75.3 bits (185), Expect = 2e-14
Identities = 37/132 (28%), Positives = 56/132 (42%), Gaps = 18/132 (13%)
Query: 167 GLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQ 226
G R EAL L ++I + + T K K R VP+ V + +
Sbjct: 29 GARWGEALGLKAEDIQEGRVTFWKT-KSGKSRTVPISERVAAML---------------K 72
Query: 227 LPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSI 286
RG L F+ ++ + L P H LRH+FA+H + NGG++ ++Q I
Sbjct: 73 RRRMRGGLFPDLYYESFRHIWKRAKIEL--PKGQATHILRHTFASHFMMNGGNIATLQHI 130
Query: 287 LGHFRLSTTQIY 298
LGH + T Y
Sbjct: 131 LGHATIEMTMRY 142
>gnl|CDD|29504 cd01183, INT_SG1_C, INT_SG1, DNA breaking-rejoining enzymes,
integrase/recombinases subgroup 1, C-terminal catalytic
domain. The CD contains mainly predicted
integrase/recombinase and site-specific XerD
recombinases. The members of this CD are found
predominantly in proteobacteria. These proteins have not
been biochemically characerised as yet..
Length = 196
Score = 72.7 bits (178), Expect = 1e-13
Identities = 47/177 (26%), Positives = 68/177 (38%), Gaps = 26/177 (14%)
Query: 148 ETKWIDARNSAILYLLYGCGLRISEALSLT----PQNIMDDQSTLRI-QGKGDKIRIVPL 202
+ AR +L LLY GLRISE + T + L + GKG K R VP+
Sbjct: 20 QDPEHAARLLFLLALLYSTGLRISELAAATGPDLEAFVQGGGWWLYVPVGKGGKERRVPV 79
Query: 203 LPSVRKAILEY---YDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQR-YIRQLRRYLGLPL 258
+ A+ Y L P + +PL + G+ R ++R G
Sbjct: 80 SDELLAALARYRQARGLPP-EPAAGEAVPLLGRHKSAGGGGGLSSAQLYRIVKRVFGAAA 138
Query: 259 ----------------STTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYT 299
+ + H LRH+ A+H L+ G L +Q LGH + TT Y
Sbjct: 139 DRLQADGFEEDAAQLRAASTHWLRHTHASHDLAAGVPLEHVQDNLGHASIDTTSRYL 195
>gnl|CDD|29510 cd01189, INT_phiLC3_C, phiLC3 phage and phage-related integrases,
site-specific recombinases, DNA breaking-rejoining
enzymes, C-terminal catalytic domain. This CD includes
various bacterial (mainly gram positive) and phage
integrases, including those similar to Lactococcus phage
phiLC3, TPW22, Tuc2009, BK5-T, A2, bIL285, bIL286,
bIL311, ul36 and phi g1e; Staphylococcus aureus phage
phi13 and phi42; Oenococcus oeni phage fOg44;
Streptococcus thermophilus phage O1205 and Sfi21; and
Streptococcus pyogenes phage T12 and T270..
Length = 191
Score = 72.2 bits (177), Expect = 2e-13
Identities = 49/195 (25%), Positives = 84/195 (43%), Gaps = 27/195 (13%)
Query: 129 LNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTL 188
L +++ L++ + H + +K + + LL GLRI EAL+LT +I + +T+
Sbjct: 3 LTKEELKKLLEYLKKHENSFSKLL-------ILLLAYTGLRIGEALALTWSDIDFENNTI 55
Query: 189 RIQ-------GKGDK--------IRIVPLLPSVRKAILEYYDLCPFDLNLNI---QLPLF 230
I G IR +PL + EY L I +F
Sbjct: 56 TINKTWDYKTGGYIFKPPKTKSSIRTIPLDKKTIAILKEYKKEQKKYLLGEINNDDELVF 115
Query: 231 RGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHF 290
GK P + ++++ + G+P T H LRH+ A+ LL G ++ + LGH
Sbjct: 116 TNKGGKISTPSTINKRLKRICKKAGIP-KITFHGLRHTHASLLLEAGVSIKYVSERLGHA 174
Query: 291 RLSTT-QIYTNVNSK 304
+STT Y+++ +
Sbjct: 175 DISTTLDTYSHLLPE 189
>gnl|CDD|29508 cd01187, INT_SG4, INT_SG4, DNA breaking-rejoining enzymes,
integrase/recombinases subgroup 4, N- and C-terminal
domains. The CD contains mainly predicted bacterial
integrase/recombinases for which not much biochemical
characterization is available..
Length = 299
Score = 69.9 bits (171), Expect = 8e-13
Identities = 52/242 (21%), Positives = 86/242 (35%), Gaps = 17/242 (7%)
Query: 71 IRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALN 130
+ + + + + L ++ F ++ ++ TE ++ + P
Sbjct: 46 ALRWAASPPSAQPATWA--GRLGVVRRFARHRRRADPRTEVPPADLFPRRPRRPTPYIYT 103
Query: 131 EKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRI 190
+++ L+ L + LL GLR+ EAL L ++ D L +
Sbjct: 104 DEEIQRLLAAALQLPPTSGLR-PWTYRTLFGLLAVTGLRLGEALRLRLSDVDLDSGILTV 162
Query: 191 -QGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPG---VFQRY 246
K K R+VPL S R A+ +Y L F RG L+ G VF
Sbjct: 163 RDSKFGKSRLVPLHASTRAALRDYLARRDRLLPAPDSSAFFVSSRGGRLSYGGHRVFYAL 222
Query: 247 IRQLRRYLGLPLSTTA--HTLRHSFATHLLS----NGGD----LRSIQSILGHFRLSTTQ 296
R++ H LRH FA L+ G D L + + LGH ++ T
Sbjct: 223 SREIGLRGWAQRGRGPRLHDLRHRFAVTRLTRWYRAGADVERKLPVLATYLGHANITDTY 282
Query: 297 IY 298
Y
Sbjct: 283 WY 284
>gnl|CDD|29518 cd01197, INT_FimBE_C, FimB and FimE and related proteins, DNA
breaking-rejoining enzymes, integrase/recombinases,
catalytic domain. This CD includes those proteins
similar to E.coli FimE and FimB regulatory proteins and
Proteus mirabilis MrpI..
Length = 180
Score = 61.9 bits (150), Expect = 2e-10
Identities = 47/156 (30%), Positives = 71/156 (45%), Gaps = 10/156 (6%)
Query: 154 ARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQG-KGDKIRIVPLLPSVRKAILE 212
AR+ ++ L++ GLR+SEA L +I + + I+ KG PL +A+
Sbjct: 24 ARDYCLMLLMFRHGLRVSEACGLKLSDIDLESRQIYIRRLKGGFSTTHPLRDDELEALKN 83
Query: 213 YYDLCPFDLNLNIQLP----LFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHS 268
+ ++ LP +F RG PL+ + IR+L GL + H LRH+
Sbjct: 84 W-----LEIRAWKGLPDSDWIFLSRRGGPLSRQQVYKLIRRLGAQAGLSIKVHPHMLRHA 138
Query: 269 FATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSK 304
L + G D R IQ LGH + T IYT N+
Sbjct: 139 CGYALANQGADTRLIQDYLGHRNIRHTVIYTASNAA 174
>gnl|CDD|29500 cd00799, INT_Cre, Cre recombinase, C-terminal catalytic domain.
Cre-like recombinases belong to the superfamily of DNA
breaking-rejoining enzymes, which share the same fold in
their catalytic domain and the overall reaction
mechanism. The bacteriophage P1 Cre recombinase
maintains the circular phage replicon in a monomeric
state by catalyzing a site-specific recombination
between two loxP sites. The catalytic core domain of
Cre recombinase is linked to a more divergent helical
N-terminal domain, which interacts primarily with the
DNA major groove proximal to the crossover region..
Length = 287
Score = 58.4 bits (141), Expect = 2e-09
Identities = 56/289 (19%), Positives = 104/289 (35%), Gaps = 44/289 (15%)
Query: 35 TLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTE--IRAFISKRRTQKIGDRSLKRSL 92
T ++Y D R+F A+ T L + + +++ + ++ R L
Sbjct: 3 TRKAYLSDWRRFA---AWCQAHGRT-----PLPASPETVTLYLTDL-ADSLAPSTISRRL 53
Query: 93 SGIKSFLKYLKKRKITTESNILN--MRNLKKSNSLPRALNEKQALTL----VDNVLLHTS 146
S + + +S ++ +R +++ + P+ +QAL + +D +
Sbjct: 54 SALSQLHRR-SGLPSPADSPLVRLVLRGIRREEARPK----RQALAILPEDLDKLRSLLD 108
Query: 147 HETKWIDARNSAILYLLYGCGLRISEALSLTPQNI-MDDQSTLRI---QGKGDK------ 196
D R+ A+L L + LR SE + L +++ D L + + K D+
Sbjct: 109 ESDTLRDLRDLALLLLGFAGLLRRSELVRLRWEDLTFTDGGGLLVTLRRSKTDQSGLGVL 168
Query: 197 IRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKP------LNPGVFQRYIRQL 250
I PL +A+ + + PLFR I L+ R +++L
Sbjct: 169 KLIPPLTTCPVRALERWLEAARIPKG-----PLFRRIDRWGVLGPGALSDNSLNRILKRL 223
Query: 251 RRYLGLPLST-TAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIY 298
GL + + H+LR FAT G L I Y
Sbjct: 224 AEAAGLRSGSWSGHSLRRGFATEAARAGYSLLEIMRQGRWRSPKMVSRY 272
>gnl|CDD|29515 cd01194, INT_Tn554A_C, Tn544A and related transposases, DNA
breaking-rejoining enzymes, integrase/recombinases,
C-terminal catalytic domain. This CD includes various
bacterial transposases similar to TnpA from transposon
Tn554..
Length = 186
Score = 56.5 bits (136), Expect = 1e-08
Identities = 40/155 (25%), Positives = 71/155 (45%), Gaps = 15/155 (9%)
Query: 154 ARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGD----------KIRIVPLL 203
R+ + LLY GLRI EAL L ++I ++ + + + D + R +P+
Sbjct: 16 LRDKFLFALLYETGLRIGEALGLRIEDIDLAENQIWLVPREDNANGARAKSGRERRIPVS 75
Query: 204 PSVRKAILEY--YDLCPFDLNLN-IQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLST 260
+ ++Y +L + + + + G +GKPLN +R+L++ G+
Sbjct: 76 QYLIDLYVDYVTEIYYLEELESDYVFVNVKGGNQGKPLNYTDVYDLVRRLKKKTGIDF-- 133
Query: 261 TAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTT 295
T H RH+ AT L+ G + + LGH + TT
Sbjct: 134 TPHMFRHTHATELIRAGWSIEVVADRLGHAHVQTT 168
>gnl|CDD|145844 pfam02899, Phage_integr_N, Phage integrase, N-terminal SAM-like
domain.
Length = 83
Score = 55.4 bits (134), Expect = 2e-08
Identities = 29/86 (33%), Positives = 51/86 (59%), Gaps = 6/86 (6%)
Query: 21 WLQNLEIERGLSKLTLQSYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRT 80
+L+ L +ERGLS T+++Y D + FL FLA ++ QL+ ++RAF+++
Sbjct: 4 FLEYLSLERGLSPNTVRAYRRDLKAFLKFLA------EGGLSLDQLTTDDVRAFLAELLR 57
Query: 81 QKIGDRSLKRSLSGIKSFLKYLKKRK 106
+ + SL R LS ++SF ++LK+
Sbjct: 58 EGLSAASLARRLSALRSFFQFLKREG 83
>gnl|CDD|29520 cd01199, INT_Tn1545_C, Tn1545-related conjugative transposon
integrases, site-specific recombinases, DNA
breaking-rejoining enzymes, C-terminal catalytic domain.
This CD includes bacterial (gram positive) and phage
integrases, including those similar to Tn1545, Tn5252,
and Tn5276 conjugative transposon integrases and
Lactobacillus phage phi adh integrase..
Length = 205
Score = 54.2 bits (130), Expect = 6e-08
Identities = 42/176 (23%), Positives = 65/176 (36%), Gaps = 25/176 (14%)
Query: 154 ARNSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDK----------------- 196
+ IL L+ G+RI E L+L ++I + + I G D
Sbjct: 21 QLYADILEFLFLTGMRIGELLALQEKDIDFENKLINIDGTLDSHTGKEENGYKDTPKTKS 80
Query: 197 -IRIVPLLPSVRKAILEYYDLCPFDLNLNIQLP---LFRGIRGKP--LNPGVFQRYIRQL 250
IR + L + I + FD LF +G P L P + + L
Sbjct: 81 SIRTISLSERAVEIIKRFIKRNKFDKFNPDYKDSDFLFTNKKGNPLDLGPINSKILSKFL 140
Query: 251 RRYL-GLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTT-QIYTNVNSK 304
+ T H RH+ + L G L++I +GH TT +IY++V K
Sbjct: 141 KDLGSQSKKHVTTHIFRHTHISFLAEEGVPLKAIMDRVGHSDGKTTLRIYSHVTEK 196
>gnl|CDD|29507 cd01186, INT_SG3_C, INT_SG3, DNA breaking-rejoining enzymes,
integrase/recombinases subgroup 3, catalytic domain. The
CD contains various predicted bacterial and phage
integrase/recombinase sequences for which not much
experimental characterization is available..
Length = 180
Score = 52.1 bits (125), Expect = 2e-07
Identities = 39/170 (22%), Positives = 67/170 (39%), Gaps = 13/170 (7%)
Query: 150 KWIDARNSAILYLLYGCG----LRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPS 205
K +S YLL+ G LRIS+ L+L +++ D+ + K K + + L P
Sbjct: 16 KDYLKNHSERNYLLFLIGINTGLRISDILALKVKDVRGDERISIKEKKTGKRKRIYLNPI 75
Query: 206 VRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRY--IRQLRRYLGLPLSTTAH 263
+++ +L Y L LF+ +G Q Y +++ +G+ T H
Sbjct: 76 LKEELLYYIKD------LEENEYLFQSRKGGNRPITRQQAYRILKKAAEQVGIDNIGT-H 128
Query: 264 TLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEI 313
TLR +F H D+ + I H + T Y +N +
Sbjct: 129 TLRKTFGYHYYKQTKDIALLMEIFNHSSPAITLRYIGINQDEIDKQLDNF 178
>gnl|CDD|29517 cd01196, INT_VanD, VanD integrase, IntD, and related integrases,
DNA breaking-rejoining enzymes, integrase/recombinases,
N- and C-terminal domains. This CD includes various
bacterial integrases including those similar to IntD, a
putative integrase-like protein, a component of the vanD
glycopeptide resistance cluster in Enterococcus faecium
BM4339. Members of this CD are predominantly bacterial
in origin..
Length = 263
Score = 49.2 bits (117), Expect = 2e-06
Identities = 38/141 (26%), Positives = 67/141 (47%), Gaps = 8/141 (5%)
Query: 159 ILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCP 218
+++ L G R+SE + + +++ I KG KIR + + ++R L++
Sbjct: 112 VVWFLAATGARVSELIHIKVEHV--QTGYADIYSKGGKIRRLYIPKNLRVEALKWLK--- 166
Query: 219 FDLNLNIQLPLFRGIRGKPLNP-GVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNG 277
+LNL +F GKP+ G+ Q+ +Y P H+ RH FA + L+
Sbjct: 167 -ELNL-DSGYIFLNRFGKPITARGIAQQLKNYAAKYKMNPRVVYPHSFRHLFAKNFLAKY 224
Query: 278 GDLRSIQSILGHFRLSTTQIY 298
DL + ++GH + TT+IY
Sbjct: 225 NDLALLADLMGHESIETTRIY 245
>gnl|CDD|29502 cd00801, INT_P4, Bacteriophage P4 integrase. P4-like integrases are
found in temperate bacteriophages, integrative plasmids,
pathogenicity and symbiosis islands, and other mobile
genetic elements. They share the same fold in their
catalytic domain and the overall reaction mechanism with
the superfamily of DNA breaking-rejoining enzymes. The
P4 integrase mediates integrative and excisive
site-specific recombination between two sites, called
attachment sites, located on the phage genome and the
bacterial chromosome. The phage attachment site is often
found adjacent to the integrase gene, while the host
attachment sites are typically situated near tRNA
genes..
Length = 357
Score = 46.8 bits (111), Expect = 7e-06
Identities = 42/231 (18%), Positives = 79/231 (34%), Gaps = 16/231 (6%)
Query: 62 TIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKK 121
I +++ ++ + +R + + +R +K +Y R + + ++R
Sbjct: 112 PITEITARDLLDVL-RRIEARGALETARRVRQRLKQVFRYAIARGLIEANPAADLRGADG 170
Query: 122 SNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQNI 181
+ +AL+ + + + L LL G+R E I
Sbjct: 171 APKKQH----DRALSPDELPEFLQALDAASGSPVTRLALKLLLLTGVRPGELRGARWSEI 226
Query: 182 MDDQSTLRIQG---KGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFRGIRGKPL 238
+ + I K + VPL A+LE +L + P R RGKPL
Sbjct: 227 DLENALWTIPAERMKTRRPHRVPL-SDQALALLE--ELRELSGHSEYVFPSRRD-RGKPL 282
Query: 239 NPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQSILGH 289
+ + ++++ T H LR + T L G I+ L H
Sbjct: 283 SENTLNKALKRMGYLGEW----TPHGLRRTARTWLNELGFPPDVIERQLAH 329
>gnl|CDD|30927 COG0582, XerC, Integrase [DNA replication, recombination, and
repair].
Length = 309
Score = 46.5 bits (107), Expect = 1e-05
Identities = 61/273 (22%), Positives = 107/273 (39%), Gaps = 19/273 (6%)
Query: 48 IFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKSFLKYLKKRKI 107
I L + + T+R L E + + L+ ++ F YL
Sbjct: 48 ILLEALGDLPLAEITVRDLLRAEAELRGKLETALRESTLTRVFRLAALRGFFAYLDNPGA 107
Query: 108 TTESNILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCG 167
++ K+ LP+AL ++ L++ + + + L+ G
Sbjct: 108 PLKAL---REKPKRRKKLPKALTAEEVEALLEALDRYRDALR---------LALLILLTG 155
Query: 168 LRISEALSLTPQNIMDDQSTLRIQGKGDKI---RIVPLLPSVRKAILEYYDLCPFDLNLN 224
LR+SE L L +I + T+ I+G K R VPL +A+ +Y + L
Sbjct: 156 LRVSELLGLRWSDIDLENGTIWIRGTKTKGRKERRVPLSEQALEALKKYLLIRRPREYLF 215
Query: 225 IQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQ 284
+ L + L R + + G+ T H LRH+FAT LL GGD R IQ
Sbjct: 216 LSLR-GPRLSRSALTINRLLRARAKAAKEAGIR-KITPHGLRHTFATLLL-AGGDERVIQ 272
Query: 285 SILGH-FRLSTTQIYTNVNSKNGGDWMMEIYDQ 316
+LGH +T +Y + + + + +++ +
Sbjct: 273 KLLGHASLNTTQTVYYHASDERLKEAALKLLEL 305
>gnl|CDD|29513 cd01192, INT_P22_C, P22-like integrases, site-specific
recombinases, DNA breaking-rejoining enzymes, C-terminal
catalytic domain. This CD includes various bacterial and
phage integrases, including those similar to phage
P22-like integrases, DLP12 and APSE-1..
Length = 177
Score = 44.9 bits (106), Expect = 3e-05
Identities = 36/155 (23%), Positives = 52/155 (33%), Gaps = 34/155 (21%)
Query: 157 SAILYLLYGCGLRISEALSLTPQNIMDDQSTLRI---QGKGDKIRIVPLLPSVRKAILEY 213
A+L+ L GLR SE L L + D + KG + VPL
Sbjct: 25 PAVLFAL-NTGLRRSEILGLEWSQVDLDNRVAWVRPATSKGGRAIRVPL----------- 72
Query: 214 YDLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPL----------STTAH 263
N L + + + P VF R H
Sbjct: 73 --------NDEA-LQVLKRQKAGAHKPWVFAGAGGDPRIDSKTAWRQALQRAGISDFRWH 123
Query: 264 TLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIY 298
LRH++A+ L+ +G L +Q +LGH L + Y
Sbjct: 124 DLRHTWASWLVQSGVPLYVLQELLGHSSLQMVRRY 158
>gnl|CDD|29516 cd01195, INT_Tn544B_C, Tn544B and related transposases, DNA
breaking-rejoining enzymes, integrase/recombinases,
catalytic domain. This CD includes various bacterial
transposases similar to TnpB from transposon Tn554..
Length = 195
Score = 43.8 bits (103), Expect = 6e-05
Identities = 39/162 (24%), Positives = 67/162 (41%), Gaps = 19/162 (11%)
Query: 159 ILYLLYGCGLRISEALSLTPQNIMDDQST-------LRIQGKGDKIRIVPLLPSV----R 207
+ ++ G+RIS+ L+L +++D+ I K I+P+ V +
Sbjct: 25 MTMIVQETGMRISDLLTLKKNCLLEDKDGDFFYKYYQCIWKTKIKEHIIPISKKVALLIK 84
Query: 208 KAILEYYDLCPFDLNLNIQL-PLFRGIR-GKPLNPGVFQRYIRQL------RRYLGLPLS 259
+ +L D N + L P + G G+P N F+ + +L G
Sbjct: 85 VREDKTKELSTEDNNPSEYLFPRYDGKPKGQPTNKQAFRGELNKLAYEKNIVDKSGEIYH 144
Query: 260 TTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNV 301
AH RH+ AT +++NG + IQ LGH T Y ++
Sbjct: 145 FHAHAFRHTVATRMINNGMPIHIIQKFLGHESPEMTSRYAHI 186
>gnl|CDD|29501 cd00800, INT_Lambda_C, Lambda integrase, C-terminal catalytic
domain. Lambda-type integrases catalyze site-specific
integration and excision of temperate bacteriophages and
other mobile genetic elements to and from the bacterial
host chromosome. They belong to the superfamily of DNA
breaking-rejoining enzymes, which share the same fold in
their catalytic domain and the overall reaction
mechanism. The phage lambda integrase can bridge two
different and well-separated DNA sequences called arm-
and core-sites. The C-terminal domain binds, cleaves
and re-ligates DNA strands at the core-sites, while the
N-terminal domain is largely responsible for
high-affinity binding to the arm-type sites..
Length = 162
Score = 42.6 bits (100), Expect = 2e-04
Identities = 42/149 (28%), Positives = 63/149 (42%), Gaps = 17/149 (11%)
Query: 157 SAILYLLYGCGLRISEALSLTPQNIMDDQSTLRI-QGK-GDKIRIVPLLPSVRKAILEYY 214
+ L G R+ + L + +I DD L I Q K G K+ I PL PS+R+ I
Sbjct: 22 RCAMDLALLTGQRVGDVLRMKWSDIDDDG--LHIEQSKTGAKLAI-PLSPSLREVI---- 74
Query: 215 DLCPFDLNLNIQLPLFRGIRG-KPLNPGVFQRYIRQLRRYLGL---PLSTTAHTLRHSFA 270
+ C DL+ L G K ++ R R+ R+ G+ T H +R + A
Sbjct: 75 ERCR-DLSRVSSPYLVHTRPGGKQVSAKTLSRAFRKARKAAGVKWGGDPPTFHDIR-AKA 132
Query: 271 THLLSNGGDLRSIQSILGHFRLSTTQIYT 299
G + Q++LGH T+IY
Sbjct: 133 ASDYEEQG--KDAQALLGHKDEKMTKIYR 159
>gnl|CDD|29505 cd01184, INT_SG2_C, INT_SG2, DNA breaking-rejoining enzymes,
integrase/recombinases subgroup 2, C-terminal catalytic
domain. The CD contains mainly predicted
integrase/recombinases and phage-related integrases.
Some have N-terminal domains, which show little sequence
similarity to each other. Members of this subgroup are
predominantly found in proteobacteria..
Length = 181
Score = 42.2 bits (99), Expect = 2e-04
Identities = 31/145 (21%), Positives = 51/145 (35%), Gaps = 20/145 (13%)
Query: 167 GLRISEALSLTPQNI--MDDQSTLRI--QGKGDKI------RIVPLLPS-VRKAILEYYD 215
G R++E L +I D + I + + R +P+ P + L+Y +
Sbjct: 37 GARVNEIAQLQVDDIREEDGVPCIDITNDDEDQSLKNAASRRTIPVHPELIELGFLDYVE 96
Query: 216 LCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGL----PLSTTAHTLRHSFAT 271
LF + G + RYL + H+ RH+F T
Sbjct: 97 ----ARRAAGHKRLFPDLPAGK-TGGYGSAVSKWFSRYLKKLGLKDKGKSFHSFRHTFIT 151
Query: 272 HLLSNGGDLRSIQSILGHFRLSTTQ 296
L + G I +I+GH +TT
Sbjct: 152 ELRNAGVSRELIAAIMGHEEGTTTF 176
>gnl|CDD|29519 cd01198, INT_ASSRA_C, Archaeal site-specific recombinase A (ASSRA),
DNA breaking-rejoining enzymes, integrase/recombinases,
C-terminal catalytic domain. Members of this CD are
archael in origin. No biochemical characterization is
available for the proteins of this subgroup at this
point..
Length = 186
Score = 40.3 bits (94), Expect = 8e-04
Identities = 38/175 (21%), Positives = 65/175 (37%), Gaps = 19/175 (10%)
Query: 158 AILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIR---IVPLLPSVRKAILEYY 214
A++ L G+R E ++L +++ D+ TL ++ +K + P L + +
Sbjct: 21 AVIVGLAKTGIRRGELINLDRRDVNLDKPTLYLKPASNKRSNRTLFPDLET--ELFRWLA 78
Query: 215 DLCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLP-------LSTTAHTLRH 267
+ LF G + + + + R G + T H RH
Sbjct: 79 IRPRTTSPAD---ALFIGTQDGWGCRRLVYEMVTGMARRHGEHRPWGDLEENFTPHCFRH 135
Query: 268 SFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQTHPSIT 322
F T L GGD +Q + G R YT+ GD + E Y + PS+
Sbjct: 136 FFTTWLRRRGGDRGVVQELRGDSRDEAIDTYTH----IWGDELREAYLKHIPSLG 186
>gnl|CDD|29497 cd00796, INT_Rci, Rci recombinase, C-terminal catalytic domain.
Rci enzymes are found in IncI1 incompatibility group
plasmids such as R64. These recombinases belong to the
superfamily of DNA breaking-rejoining enzymes, which
share the same fold in their catalytic domain and the
overall reaction mechanism. The R64 Rci recombinase
mediates site specific recombination at the highly
mobile DNA segments called shufflon located in the
C-terminal region of the pilV gene, which determines the
recipient specificity in liquid mating. This gene
encodes a thin pilus component that recognizes
recipient's receptors required for liquid mating. The
recombination occurs between any of the seven inverted
repeats that separate four DNA segments of the shufflon.
The segments can be inverted independently or in groups,
resulting in a complex DNA rearrangement. The catalytic
domain of Rci is linked to a variable N-terminal domain,
whose function is unknown..
Length = 206
Score = 36.0 bits (83), Expect = 0.014
Identities = 32/140 (22%), Positives = 53/140 (37%), Gaps = 15/140 (10%)
Query: 167 GLRISEALSLTPQNI-MDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNI 225
+R E LSL + + + + K R VPL A+L+ P D
Sbjct: 77 AMRRGEILSLRWEQVDLKKRVAHLPDTKNGTSRDVPLSKRAV-ALLQMLPKVPDDG---- 131
Query: 226 QLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLSNGGDLRSIQS 285
P+F P+ R+ + GL H LRH + L G + + S
Sbjct: 132 --PVF------PITSDSVDAAFRRAKERAGLE-DLHFHDLRHEATSRLFEKGLSIMEVAS 182
Query: 286 ILGHFRLSTTQIYTNVNSKN 305
I GH + YT++++++
Sbjct: 183 ISGHRDWRMLKRYTHLSAED 202
>gnl|CDD|29512 cd01191, INT_phiCTX_C, phiCTX phage and phage-related integrases,
site-specific recombinases, DNA breaking-rejoining
enzymes, C-terminal catalytic domain. This CD includes
various phage and bacterial integrases, including those
similar to phage integrases: Bordetella and Pseudomonas
phiCTX; E. coli Rac, Qin, and Shiga toxin 2 933W; and
Salmonella typhimurium LT2 Gifsy-2 and Fels-1; and a
putative pore-forming cytotoxin integrase from Vibrio
parahaemolyticus O3:K6..
Length = 196
Score = 31.5 bits (71), Expect = 0.35
Identities = 36/171 (21%), Positives = 61/171 (35%), Gaps = 34/171 (19%)
Query: 167 GLRISEALSLTPQNIMDDQSTLRI-------QGKGDK----IRIVPLLPSVRKAILEYYD 215
GLR SE ++L +++ ++ T+ + K K R V L P A+ E
Sbjct: 33 GLRPSELIALAWEDVDLERGTVYVRRALVRGIFKVPKTKAGTRDVDLNPPALAALKEQAK 92
Query: 216 LCPFDLNLNIQLPLFRGIRGKPLNPG-VFQ--------RYIRQLRRYLGLPL-------S 259
L I + R + VF Y R+ P
Sbjct: 93 LTRLSRPHQITVLEREYGRTEKQKGTFVFHDPKTGEPWTYAVASRKSFWDPALKRAGIRY 152
Query: 260 TTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWM 310
+ +RH+FA+ +L+ G + I +GH S ++ K+ G W+
Sbjct: 153 RNPYQMRHTFASWMLTAGANPAFIADQMGH--KSAEMVF-----KHYGKWI 196
>gnl|CDD|34064 COG4342, COG4342, Uncharacterized protein conserved in archaea
[Function unknown].
Length = 291
Score = 30.4 bits (68), Expect = 0.77
Identities = 47/254 (18%), Positives = 79/254 (31%), Gaps = 28/254 (11%)
Query: 38 SYECDTRQFLIFLAFYTEEKITIQTIRQLSYTEIRAFISKRRTQKIGDRSLKRSLSGIKS 97
Y +R +L+ K + +L R ++S R + +
Sbjct: 27 GYRQISRSWLLERIVERTAKDYFERWIKLCGKTARDYLSALNRPIGSVREKDKYQKAYRL 86
Query: 98 FLKYLKKRKITTES--NILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDAR 155
F+K+L R I +E L + LK S L + + + ++ R
Sbjct: 87 FIKFLTSRGIISEEFAEKL-RKPLKVKKSNGVDL----YIPSDEEIRATEELAREY-SER 140
Query: 156 NSAILYLLYGCGLRISEALSLTPQNIMDDQSTLRIQGKGDKIRIVPLLPSVRKAILEYYD 215
+ LL G R+SEA+++ D S L G I P L R +Y
Sbjct: 141 AYLVYLLLLFSGARLSEAVAVLRN---LDHSRLYCVVNGKVICYYP-LSWSRGHKRAFYI 196
Query: 216 LCPFDLNLNIQLPLFRGIRGKPLNPGVFQRYIRQLRRYLGLPLSTTAHTLRHSFATHLLS 275
P D +R ++ QR+ + A +R +L
Sbjct: 197 FHPKD--------FAESLRKIDISYHRVQRFENRRG--------VKAKYIRKWVYNKMLE 240
Query: 276 NGGDLRSIQSILGH 289
G + I G
Sbjct: 241 LGVPEDVVDFIQGR 254
>gnl|CDD|34837 COG5240, SEC21, Vesicle coat complex COPI, gamma subunit
[Intracellular trafficking and secretion].
Length = 898
Score = 29.7 bits (66), Expect = 1.1
Identities = 23/119 (19%), Positives = 42/119 (35%), Gaps = 17/119 (14%)
Query: 72 RAFISKRRTQKIGD-RSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALN 130
A + ++GD SL+ L G Y+ + T ++ +R + L
Sbjct: 557 DACEPLFSSDELGDIPSLELELIG------YISEDSFATAFDVNQVRKFTEDEMKAINLK 610
Query: 131 EKQALTLVD----------NVLLHTSHETKWIDARNSAILYLLYGCGLRISEALSLTPQ 179
K++ T +D N + +TK+ D S +G + S + LT
Sbjct: 611 RKKSETTLDTTESVPKEDANSKADPNIKTKYADELLSIEQIKPFGQLVNSSREIILTEP 669
>gnl|CDD|34244 COG4624, COG4624, Iron only hydrogenase large subunit, C-terminal
domain [General function prediction only].
Length = 411
Score = 29.6 bits (66), Expect = 1.3
Identities = 15/55 (27%), Positives = 24/55 (43%), Gaps = 6/55 (10%)
Query: 164 YGCGLRISEALSLTPQNIMDDQSTLRIQGK--GDKIRIVPLLPSVRKAILEYYDL 216
GC + E ++ ++ + L DKI +V PSVR A+ E + L
Sbjct: 40 SGC-ITSCEVKAI---SLQSGKKVLEELEDLFCDKIVLVSNAPSVRAALAEEFGL 90
>gnl|CDD|34311 COG4695, COG4695, Phage-related protein [Function unknown].
Length = 398
Score = 29.2 bits (65), Expect = 1.9
Identities = 16/78 (20%), Positives = 25/78 (32%)
Query: 112 NILNMRNLKKSNSLPRALNEKQALTLVDNVLLHTSHETKWIDARNSAILYLLYGCGLRIS 171
IL K E AL V N +DA + ++ C +S
Sbjct: 3 PILRFAKNNKFERRSSIAPEFSALAAVANPESGAGRSGSKVDAEGAMRNPAVFSCVRVLS 62
Query: 172 EALSLTPQNIMDDQSTLR 189
EA++ P N+ +
Sbjct: 63 EAVATLPLNLYQRDNEGI 80
>gnl|CDD|132952 cd06621, PKc_MAPKK_Pek1_like, Catalytic domain of fungal Pek1-like
dual-specificity MAP kinase kinases. Protein kinases
(PKs), MAP kinase kinase(MAPKK) subfamily, fungal
Pek1-like proteins, catalytic (c) domain. PKs catalyze
the transfer of the gamma-phosphoryl group from ATP to
serine/threonine or tyrosine residues on protein
substrates. The MAPKK subfamily is part of a larger
superfamily that includes the catalytic domains of other
protein serine/threonine kinases, protein tyrosine
kinases, RIO kinases, aminoglycoside phosphotransferase,
choline kinase, and phosphoinositide 3-kinase. The
mitogen-activated protein (MAP) kinase signaling
pathways are important mediators of cellular responses
to extracellular signals. The pathways involve a triple
kinase core cascade comprising of the MAP kinase (MAPK),
which is phosphorylated and activated by a MAPK kinase
(MAPKK or MKK), which itself is phosphorylated and
activated by a MAPK kinase kinase (MAPKKK or MKKK).
Members of this group include the MAPKKs Pek1/Skh1 from
Schizosaccharomyces pombe and MKK2 from Saccharomyces
cerevisiae, and related proteins. Both fission yeast
Pek1 and baker's yeast MKK2 are components of the cell
integrity MAPK pathway. In fission yeast, Pek1
phosphorylates and activates the MAPK Pmk1/Spm1 and is
regulated by the MAPKKK Mkh1. In baker's yeast, the
pathway involves the MAPK Slt2, the MAPKKs MKK1 and
MKK2, and the MAPKKK Bck1. The cell integrity MAPK
cascade is activated by multiple stress conditions, and
is essential in cell wall construction, morphogenesis,
cytokinesis, and ion homeostasis.
Length = 287
Score = 28.9 bits (65), Expect = 2.0
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 10/63 (15%)
Query: 77 KRRTQKIGDRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSNSLPRALNEKQALT 136
K+R +IG++ L + + L YL RKI R++K SN L L K +
Sbjct: 96 KKRGGRIGEKVLGKIAESVLKGLSYLHSRKII-------HRDIKPSNIL---LTRKGQVK 145
Query: 137 LVD 139
L D
Sbjct: 146 LCD 148
>gnl|CDD|145499 pfam02387, IncFII_repA, IncFII RepA protein family. This protein
is plasmid encoded and found to be essential for plasmid
replication.
Length = 279
Score = 28.9 bits (65), Expect = 2.0
Identities = 29/118 (24%), Positives = 45/118 (38%), Gaps = 19/118 (16%)
Query: 15 LKERQNWLQNLEIERGLSKLTLQSYECDTRQFLIFLAF-YTEEKITIQTIR-------QL 66
K++ W ++GL LTL ++F I AF Y E+ R +L
Sbjct: 172 RKQQLEWENKKLKKKGLIPLTLDEARRRAKEFHIERAFSYRTERKAFGKKRRRARKLAKL 231
Query: 67 SYTEIRAFISKRRTQKIG-DRSLKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKSN 123
+IR I ++ K L G+ K+K+ E N N+R L +S
Sbjct: 232 DEKDIRKKILNALVKEYSKGELTKMGLKGL--------KKKVDIEYN--NLRKLAESP 279
>gnl|CDD|153336 cd07652, F-BAR_Rgd1, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Saccharomyces cerevisiae
Rho GTPase activating protein Rgd1 and similar proteins.
F-BAR domains are dimerization modules that bind and
bend membranes and are found in proteins involved in
membrane dynamics and actin reorganization.
Saccharomyces cerevisiae Rgd1 is a GTPase activating
protein (GAP) with activity towards Rho3p and Rho4p,
which are involved in bud growth and cytokinesis,
respectively. At low pH, S. cerevisiae Rgd1 is required
for cell survival and the activation of the protein
kinase C pathway, which is important in cell integrity
and the maintenance of cell shape. It contains an
N-terminal F-BAR domain and a C-terminal Rho GAP domain.
The F-BAR domain of S. cerevisiae Rgd1 binds to
phosphoinositides and plays an important role in the
localization of the protein to the bud tip/neck during
the cell cycle. F-BAR domains form banana-shaped dimers
with a positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 234
Score = 28.5 bits (64), Expect = 2.7
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 88 LKRSLSGIKSFLKYLKKRKITTESNILNMRNLKKS 122
LK+S++ K F +LKKR E + ++ L ++
Sbjct: 14 LKQSIASAKEFATFLKKRAAIEEEHARGLKKLART 48
>gnl|CDD|133191 cd05060, PTKc_Syk_like, Catalytic domain of Spleen Tyrosine
Kinase-like Protein Tyrosine Kinases. Protein Tyrosine
Kinase (PTK) family; Spleen Tyrosine Kinase (Syk)
subfamily; catalytic (c) domain. The Syk subfamily is
composed of Syk, ZAP-70, Shark, and similar proteins.
The PTKc family is part of a larger superfamily that
includes the catalytic domains of other kinases such as
protein serine/threonine kinases, RIO kinases, and
phosphoinositide 3-kinase (PI3K). PTKs catalyze the
transfer of the gamma-phosphoryl group from ATP to
tyrosine (tyr) residues in protein substrates. Syk
subfamily kinases are cytoplasmic (or nonreceptor) tyr
kinases containing two Src homology 2 (SH2) domains
N-terminal to the catalytic tyr kinase domain. They are
involved in the signaling downstream of activated
receptors (including B-cell, T-cell, and Fc receptors)
that contain ITAMs (immunoreceptor tyr activation
motifs), leading to processes such as cell
proliferation, differentiation, survival, adhesion,
migration, and phagocytosis. Syk is important in B-cell
receptor (BCR) signaling, while Zap-70 is primarily
expressed in T-cells and NK cells, and is a crucial
component in T-cell receptor (TCR) signaling. Syk also
plays a central role in Fc receptor-mediated
phagocytosis in the adaptive immune system. Shark is
exclusively expressed in ectodermally derived epithelia,
and is localized preferentially to the apical surface of
the epithelial cells, it may play a role in a signaling
pathway for epithelial cell polarity.
Length = 257
Score = 28.1 bits (63), Expect = 3.3
Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 15/67 (22%)
Query: 92 LSGIKSFLKYLKKRKITTESNILN--------MRNLKKSNSLPRALNEKQALTLVDNVLL 143
L+ + LKYLKKR+ S++ M L+ + + R L + NVLL
Sbjct: 76 LAPLGPLLKYLKKRREIPVSDLKELAHQVAMGMAYLESKHFVHRDLAAR-------NVLL 128
Query: 144 HTSHETK 150
H+ K
Sbjct: 129 VNRHQAK 135
>gnl|CDD|37082 KOG1871, KOG1871, KOG1871, Ubiquitin-specific protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 420
Score = 27.7 bits (61), Expect = 4.3
Identities = 10/69 (14%), Positives = 21/69 (30%)
Query: 257 PLSTTAHTLRHSFATHLLSNGGDLRSIQSILGHFRLSTTQIYTNVNSKNGGDWMMEIYDQ 316
L + + +L +S+ + +T Y S++ I D
Sbjct: 333 TLKISKNCFSQGLKIRILIATRPYKSLAVVYHTGTSATVGHYLEDVSRSVPSGWQRIDDA 392
Query: 317 THPSITQKD 325
+ Q+D
Sbjct: 393 LILFVAQED 401
>gnl|CDD|37021 KOG1810, KOG1810, KOG1810, Cell cycle-associated protein [Cell cycle
control, cell division, chromosome partitioning].
Length = 1417
Score = 27.6 bits (61), Expect = 4.7
Identities = 16/99 (16%), Positives = 36/99 (36%), Gaps = 8/99 (8%)
Query: 80 TQKIGDRSLKRSLSGIKSFLKYLKKRKITTES----NILNMRNLKKSNSLPRALNEKQAL 135
++ R + ++ ++ L Y KI+++ + L + + + P +
Sbjct: 1212 QNQLAQRCSEDHITHQEAGLAYGLAEKISSKMLELYHFLPDEDEEIRSKAPFGQTKVYLR 1271
Query: 136 TLVDNVLLHTSHE----TKWIDARNSAILYLLYGCGLRI 170
T V L +H T + + I + CGL +
Sbjct: 1272 TQAWEVCLARNHLRFILTHDFEDVFNDIGLVEDFCGLVL 1310
>gnl|CDD|39057 KOG3853, KOG3853, KOG3853, Inositol monophosphatase [Signal
transduction mechanisms].
Length = 350
Score = 27.3 bits (60), Expect = 6.1
Identities = 26/94 (27%), Positives = 37/94 (39%), Gaps = 7/94 (7%)
Query: 121 KSNSLPRALNEKQALTLVDN---VLLHTSHETKWIDARNSAILYLLYGCGLRIS-EALSL 176
K N P + L LV+ + LHT+ KW AIL L G + + +
Sbjct: 253 KMNIEPAGGAGYKVLRLVNGTAELYLHTTAIKKWDICAGDAILRALGGAMTTLEGQPIRY 312
Query: 177 TPQNIMDDQSTL-RIQGKGDKIRIVPLLPSVRKA 209
+PQ I + L I+ +K I LP K
Sbjct: 313 SPQKINNFTGLLAEIKNSHEK--ITLKLPKKNKL 344
>gnl|CDD|99992 cd03822, GT1_ecORF704_like, This family is most closely related to
the GT1 family of glycosyltransferases. ORF704 in E.
coli has been shown to be involved in the biosynthesis
of O-specific mannose homopolysaccharides..
Length = 366
Score = 27.2 bits (61), Expect = 6.8
Identities = 18/93 (19%), Positives = 31/93 (33%), Gaps = 14/93 (15%)
Query: 190 IQGKGDKIRIVPLLPSVRKAILEYYDLCPFDLNLNIQLPLFR---GIRGKPLNPGVFQ-- 244
+ +G + +V + + + L+ L R IR + V Q
Sbjct: 26 LSARGPDVLVVSVAALYPSLLYGGEQEVVRVIVLDNPLDYRRAARAIRLSGPDVVVIQHE 85
Query: 245 ---------RYIRQLRRYLGLPLSTTAHTLRHS 268
Y+ L R LG+P+ T HT+
Sbjct: 86 YGIFGGEAGLYLLLLLRGLGIPVVVTLHTVLLH 118
>gnl|CDD|99973 cd03800, GT1_Sucrose_synthase, This family is most closely related
to the GT1 family of glycosyltransferases. The
sucrose-phosphate synthases in this family may be unique
to plants and photosynthetic bacteria. This enzyme
catalyzes the synthesis of sucrose 6-phosphate from
fructose 6-phosphate and uridine 5'-diphosphate-glucose,
a key regulatory step of sucrose metabolism. The
activity of this enzyme is regulated by phosphorylation
and moderated by the concentration of various
metabolites and light..
Length = 398
Score = 27.1 bits (61), Expect = 7.3
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 249 QLRRYLGLPLSTTAHTL 265
L R LG+PL T H+L
Sbjct: 118 LLARRLGIPLVHTFHSL 134
>gnl|CDD|32672 COG2844, GlnD, UTP:GlnB (protein PII) uridylyltransferase
[Posttranslational modification, protein turnover,
chaperones].
Length = 867
Score = 26.8 bits (59), Expect = 9.0
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 138 VDNVLLHTSHETKWIDARNSAILYLLYGCGLRISEA 173
+D +LL T W++ + LYLL+ GL + +
Sbjct: 86 IDLLLLSPQKLTDWLEQKIERFLYLLWDLGLEVGHS 121
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.320 0.136 0.391
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,822,373
Number of extensions: 197017
Number of successful extensions: 597
Number of sequences better than 10.0: 1
Number of HSP's gapped: 563
Number of HSP's successfully gapped: 51
Length of query: 328
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 234
Effective length of database: 4,232,491
Effective search space: 990402894
Effective search space used: 990402894
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: 57 (25.7 bits)