RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780490|ref|YP_003064903.1| site-specific tyrosine
recombinase XerC [Candidatus Liberibacter asiaticus str. psy62]
(67 letters)
>gnl|CDD|178942 PRK00236, xerC, site-specific tyrosine recombinase XerC; Reviewed.
Length = 297
Score = 109 bits (275), Expect = 2e-25
Identities = 35/56 (62%), Positives = 45/56 (80%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPS 59
T H LRHSFATHLL +GGDLR++Q +LGH+ LSTTQIYT+V+ + + E+YD HP
Sbjct: 241 TPHKLRHSFATHLLESGGDLRAVQELLGHASLSTTQIYTHVDFQHLAEVYDAAHPR 296
>gnl|CDD|162771 TIGR02224, recomb_XerC, tyrosine recombinase XerC. The phage
integrase family describes a number of recombinases with
tyrosine active sites that transiently bind covalently
to DNA. Many are associated with mobile DNA elements,
including phage, transposons, and phase variation loci.
This model represents XerC, one of two closely related
chromosomal proteins along with XerD (TIGR02225). XerC
and XerD are site-specific recombinases which help
resolve chromosome dimers to monomers for cell division
after DNA replication. In species with a large
chromosome and homologs of XerC on other replicons, the
chomosomal copy was preferred for building this model.
This model does not detect all XerC, as some apparent
XerC examples score in the gray zone between trusted
(450) and noise (410) cutoffs, along with some XerD
examples. XerC and XerD interact with cell division
protein FtsK.
Length = 295
Score = 102 bits (257), Expect = 2e-23
Identities = 34/55 (61%), Positives = 44/55 (80%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHP 58
H LRHSFATHLL NG DLR++Q +LGH+ LSTTQIYT+V+ + + ++YDQ HP
Sbjct: 237 HPHALRHSFATHLLENGADLRAVQELLGHASLSTTQIYTHVDFQHLAKVYDQAHP 291
>gnl|CDD|162772 TIGR02225, recomb_XerD, tyrosine recombinase XerD. The phage
integrase family describes a number of recombinases with
tyrosine active sites that transiently bind covalently
to DNA. Many are associated with mobile DNA elements,
including phage, transposons, and phase variation loci.
This model represents XerD, one of two closely related
chromosomal proteins along with XerC (TIGR02224). XerC
and XerD are site-specific recombinases which help
resolve chromosome dimers to monomers for cell division
after DNA replication. In species with a large
chromosome and with homologs of XerD on other replicons,
the chomosomal copy was preferred for building this
model. This model does not detect all XerD, as some
apparent XerD examples score below the trusted and noise
cutoff scores. XerC and XerD interact with cell division
protein FtsK.
Length = 291
Score = 98.8 bits (247), Expect = 3e-22
Identities = 33/55 (60%), Positives = 44/55 (80%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHP 58
+ HTLRHSFATHLL NG DLR +Q +LGH+ +STTQIYT+V +R+ E++ + HP
Sbjct: 235 SPHTLRHSFATHLLENGADLRVVQELLGHADISTTQIYTHVARERLKEVHKKHHP 289
>gnl|CDD|178959 PRK00283, xerD, site-specific tyrosine recombinase XerD; Reviewed.
Length = 299
Score = 94.5 bits (236), Expect = 5e-21
Identities = 32/53 (60%), Positives = 44/53 (83%)
Query: 6 HTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHP 58
H LRH+FATHLL++G DLR +Q +LGHS +STTQIYT+V ++R+ E++ Q HP
Sbjct: 245 HVLRHAFATHLLNHGADLRVVQELLGHSDISTTQIYTHVATERLKELHAQHHP 297
>gnl|CDD|179273 PRK01287, xerC, site-specific tyrosine recombinase XerC; Reviewed.
Length = 358
Score = 77.9 bits (192), Expect = 6e-16
Identities = 29/61 (47%), Positives = 41/61 (67%)
Query: 6 HTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQKDK 65
H RH+ AT +L NG D R IQ+ILGH++L TTQIYT V+ + ++ THP+ + D+
Sbjct: 268 HLFRHAMATQMLENGADTRHIQAILGHAKLETTQIYTRVSIGHLQAVHASTHPAERKADE 327
Query: 66 K 66
K
Sbjct: 328 K 328
>gnl|CDD|131303 TIGR02249, integrase_gron, integron integrase. Members of this
family are integrases associated with integrons (and
super-integrons), which are systems for incorporating
and expressing cassettes of laterally transferred DNA.
Incorporation occurs at an attI site. A super-integron,
as in Vibrio sp., may include over 100 cassettes. This
family belongs to the phage integrase family (pfam00589)
that also includes recombinases XerC (TIGR02224) and
XerD (TIGR02225), which are bacterial housekeeping
proteins. Within this family of integron integrases,
some are designated by class, e.g. IntI4, a class 4
integron integrase from Vibrio cholerae N16961.
Length = 315
Score = 71.7 bits (176), Expect = 4e-14
Identities = 28/41 (68%), Positives = 35/41 (85%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNV 44
T HTLRHSFATHLL +G D+R++Q +LGHS + TTQIYT+V
Sbjct: 260 TCHTLRHSFATHLLESGADIRTVQELLGHSDVKTTQIYTHV 300
>gnl|CDD|185315 PRK15417, PRK15417, integrase/recombinase; Provisional.
Length = 337
Score = 58.1 bits (140), Expect = 5e-10
Identities = 27/41 (65%), Positives = 34/41 (82%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNV 44
T HTLRHSFAT LL +G D+R++Q +LGHS +STT IYT+V
Sbjct: 275 TPHTLRHSFATALLRSGYDIRTVQDLLGHSDVSTTMIYTHV 315
>gnl|CDD|164996 PHA02601, int, integrase; Provisional.
Length = 333
Score = 50.5 bits (121), Expect = 9e-08
Identities = 17/36 (47%), Positives = 25/36 (69%)
Query: 6 HTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIY 41
H LRH+FA+H + NGG++ +Q ILGH+ + T Y
Sbjct: 279 HVLRHTFASHFMMNGGNILVLQRILGHATIEMTMAY 314
>gnl|CDD|179927 PRK05084, xerS, site-specific tyrosine recombinase XerS; Reviewed.
Length = 357
Score = 46.1 bits (110), Expect = 2e-06
Identities = 16/46 (34%), Positives = 23/46 (50%)
Query: 4 TAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRM 49
T H LRH+ AT L D + LGH+ TT +YT++ +
Sbjct: 304 TPHKLRHTLATRLYDATKDQVLVADQLGHTSTETTDLYTHIVNDEQ 349
>gnl|CDD|182125 PRK09870, PRK09870, tyrosine recombinase; Provisional.
Length = 200
Score = 38.4 bits (89), Expect = 4e-04
Identities = 21/51 (41%), Positives = 26/51 (50%)
Query: 6 HTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQT 56
H LRHS L + G D R IQ LGH + T YT N+ R I+D+
Sbjct: 141 HMLRHSCGFALANMGIDTRLIQDYLGHRNIRHTVWYTASNAGRFYGIWDRA 191
>gnl|CDD|182126 PRK09871, PRK09871, tyrosine recombinase; Provisional.
Length = 198
Score = 38.0 bits (88), Expect = 5e-04
Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 3 TTAHTLRHSFATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQ 62
T H LRH+ L G D R IQ LGH + T YT N+ R ++++ + I +
Sbjct: 133 THPHMLRHACGYELAERGADTRLIQDYLGHRNIRHTVRYTASNAARFAGLWERNNL-INE 191
Query: 63 KDKK 66
K K+
Sbjct: 192 KLKR 195
>gnl|CDD|177485 PHA02731, PHA02731, putative integrase; Provisional.
Length = 231
Score = 30.5 bits (68), Expect = 0.094
Identities = 16/51 (31%), Positives = 26/51 (50%), Gaps = 3/51 (5%)
Query: 6 HTLRHSFATHLLS-NGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQ 55
H+LR++ +L G D+ I GH+ L +YT +K EI+D+
Sbjct: 179 HSLRYAGINYLAKVEGIDMAIIAKFTGHANLDQIILYT--QTKAADEIFDR 227
>gnl|CDD|178345 PLN02744, PLN02744, dihydrolipoyllysine-residue acetyltransferase
component of pyruvate dehydrogenase complex.
Length = 539
Score = 25.6 bits (56), Expect = 3.3
Identities = 8/53 (15%), Positives = 24/53 (45%), Gaps = 11/53 (20%)
Query: 12 FATHLLSNGGDLRSIQSILGHSRLSTTQIYTNVNSKRMMEIYDQTHPSITQKD 64
+A+ ++++ LR++ ++L + + ++N T S+ + D
Sbjct: 2 YASRIINHSKKLRNVSNLLRREHAALVRYFSN-----------STRSSLGKGD 43
>gnl|CDD|181728 PRK09250, PRK09250, fructose-bisphosphate aldolase; Provisional.
Length = 348
Score = 25.2 bits (56), Expect = 3.3
Identities = 10/20 (50%), Positives = 14/20 (70%)
Query: 19 NGGDLRSIQSILGHSRLSTT 38
N G LR++Q +L H RL+ T
Sbjct: 45 NPGVLRNLQRLLNHGRLAGT 64
>gnl|CDD|150143 pfam09369, DUF1998, Domain of unknown function (DUF1998). This
family of proteins are functionally uncharacterized.
They are mainly found in helicase proteins so could be
RNA binding. This family includes a probable zinc
binding motif at its C-terminus.
Length = 81
Score = 24.8 bits (55), Expect = 4.5
Identities = 11/43 (25%), Positives = 13/43 (30%), Gaps = 1/43 (2%)
Query: 3 TTAHTLRHSFATHLLSNGGDLR-SIQSILGHSRLSTTQIYTNV 44
T H L + L + DL SI IY V
Sbjct: 1 TLEHALIRALPLVLGCDRSDLGESIYPEPDTDGRPGILIYDAV 43
>gnl|CDD|183991 PRK13352, PRK13352, thiamine biosynthesis protein ThiC;
Provisional.
Length = 431
Score = 24.7 bits (55), Expect = 5.2
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 3/28 (10%)
Query: 17 LSNGGDLRSI-QSILGHSRLS--TTQIY 41
LS GGDL I ++I+ S + T IY
Sbjct: 97 LSTGGDLDEIRRAIIEASPVPVGTVPIY 124
>gnl|CDD|185515 PTZ00213, PTZ00213, asparagine synthetase A; Provisional.
Length = 348
Score = 24.0 bits (52), Expect = 8.2
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 40 IYTNVNSKRMMEIYDQTH 57
IYT++N+ R+ E D H
Sbjct: 95 IYTDMNALRVEEELDNIH 112
>gnl|CDD|131779 TIGR02732, zeta_caro_desat, carotene 7,8-desaturase. Carotene
7,8-desaturase, also called zeta-carotene desaturase,
catalyzes multiple steps in the pathway from
geranylgeranyl-PP to all-trans-lycopene in plants and
cyanobacteria. A similar enzyme and pathway is found in
the green sulfur bacterium Chlorobium tepidum.
Length = 474
Score = 24.0 bits (52), Expect = 8.3
Identities = 10/17 (58%), Positives = 12/17 (70%)
Query: 11 SFATHLLSNGGDLRSIQ 27
SFA LS+GG L SI+
Sbjct: 155 SFAEWFLSHGGSLGSIK 171
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.314 0.124 0.341
Gapped
Lambda K H
0.267 0.0789 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 931,210
Number of extensions: 39001
Number of successful extensions: 101
Number of sequences better than 10.0: 1
Number of HSP's gapped: 101
Number of HSP's successfully gapped: 21
Length of query: 67
Length of database: 5,994,473
Length adjustment: 38
Effective length of query: 29
Effective length of database: 5,173,369
Effective search space: 150027701
Effective search space used: 150027701
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (22.9 bits)