RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254781079|ref|YP_003065492.1| diguanylate cyclase
[Candidatus Liberibacter asiaticus str. psy62]
(266 letters)
>gnl|CDD|143635 cd01949, GGDEF, Diguanylate-cyclase (DGC) or GGDEF domain.
Diguanylate-cyclase (DGC) or GGDEF domain: Originally
named after a conserved residue pattern, and initially
described as a domain of unknown function 1 (DUF1). This
domain is widely present in bacteria, linked to a wide
range of non-homologous domains in a variety of cell
signaling proteins. The domain shows homology to the
adenylyl cyclase catalytic domain. This correlates with
the functional information available on two
GGDEF-containing proteins, namely diguanylate cyclase
and phosphodiesterase A of Acetobacter xylinum, both of
which regulate the turnover of cyclic diguanosine
monophosphate. Together with the EAL domain, GGDEF might
be involved in regulating cell surface adhesion in
bacteria.
Length = 158
Score = 154 bits (391), Expect = 3e-38
Identities = 63/160 (39%), Positives = 87/160 (54%), Gaps = 10/160 (6%)
Query: 105 RIDCLSGLLNHSAF-------ISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAF 157
D L+GL N AF ++ L+++ DID+FKQIND +GH GD+V+
Sbjct: 1 YTDPLTGLPNRRAFEERLERLLARARRSGRPLALLLIDIDHFKQINDTYGHAAGDEVLKE 60
Query: 158 LSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIH 217
++++L V RLGG+EFA G+ +EA LA LR+ IE + G I
Sbjct: 61 VAERLRSSLRESDLVARLGGDEFAILLPGTDLEEAEALAERLREAIE--EPFFIDGQEIR 118
Query: 218 ITISAGIAE-RCHKEPISTIIYRADQALYVAKKSGRNRVV 256
+T S GIA E ++ RAD+ALY AK+SGRNRVV
Sbjct: 119 VTASIGIATYPEDGEDAEELLRRADEALYRAKRSGRNRVV 158
>gnl|CDD|32381 COG2199, COG2199, FOG: GGDEF domain [Signal transduction
mechanisms].
Length = 181
Score = 138 bits (348), Expect = 2e-33
Identities = 64/179 (35%), Positives = 98/179 (54%), Gaps = 11/179 (6%)
Query: 89 ILKELFISYNRISQLSRIDCLSGLLNHSAF-------ISSLGSYNEKLSIVFFDIDYFKQ 141
+L L + R+ +L+ D L+GL N AF ++ + E L+++ D+D+FKQ
Sbjct: 5 LLTRLRKAEERLERLALHDPLTGLPNRRAFEERLERALARARRHGEPLALLLLDLDHFKQ 64
Query: 142 INDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRK 201
IND +GH GD+V+ ++ +L V RLGG+EFA G+S +EAA LA +R
Sbjct: 65 INDTYGHAAGDEVLREVARRLRSNLREGDLVARLGGDEFAVLLPGTSLEEAARLAERIRA 124
Query: 202 IIENSQINISSGPSIHITISAGIAERCHKEPIS--TIIYRADQALYVAKKSGRNRVVCF 258
+E + G + +T+S G+A ++ RAD ALY AK++GRNRVV F
Sbjct: 125 ALE--EPFFLGGEELRVTVSIGVALYPEDGSDDAELLLRRADLALYRAKRAGRNRVVVF 181
>gnl|CDD|144545 pfam00990, GGDEF, GGDEF domain. This domain is found linked to a
wide range of non-homologous domains in a variety of
bacteria. It has been shown to be homologous to the
adenylyl cyclase catalytic domain and has diguanylate
cyclase activity. This observation correlates with the
functional information available on two GGDEF-containing
proteins, namely diguanylate cyclase and
phosphodiesterase A of Acetobacter xylinum, both of
which regulate the turnover of cyclic diguanosine
monophosphate.
Length = 159
Score = 124 bits (314), Expect = 2e-29
Identities = 58/159 (36%), Positives = 85/159 (53%), Gaps = 8/159 (5%)
Query: 104 SRIDCLSGLLNHSAFISSLGS------YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAF 157
+ D L+GL N F L L+++ D+D FK+IND +GH VGD+V+
Sbjct: 1 AAHDPLTGLPNRRYFEEELEQELQRARRQSPLALLLLDLDNFKRINDTYGHAVGDEVLQE 60
Query: 158 LSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINIS-SGPSI 216
++ +L V RLGG+EFA +S + A LA +R+++ +I + SG +
Sbjct: 61 VAQRLSSSLRRSDLVARLGGDEFAILLPDTSLEGAQELAERIRRLLAALKIPHTLSGLPL 120
Query: 217 HITISAGIAE-RCHKEPISTIIYRADQALYVAKKSGRNR 254
++TIS GIA E ++ RADQALY AK GRNR
Sbjct: 121 YVTISIGIAAYPNDGEDAEDLLKRADQALYQAKNQGRNR 159
>gnl|CDD|33501 COG3706, PleD, Response regulator containing a CheY-like receiver
domain and a GGDEF domain [Signal transduction
mechanisms].
Length = 435
Score = 124 bits (312), Expect = 3e-29
Identities = 65/177 (36%), Positives = 96/177 (54%), Gaps = 11/177 (6%)
Query: 90 LKELFISYNRISQLSRIDCLSGLLNHSAFISSLGSY-------NEKLSIVFFDIDYFKQI 142
++L S R+ +L+ +D L+GL N F L LS++ DID FK+I
Sbjct: 256 ERQLRESLERLQELALVDGLTGLFNRRYFDEHLADLWKRALREGRPLSLLMLDIDDFKEI 315
Query: 143 NDNFGHPVGDKVIAFLSDQLV-VVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRK 201
ND +GH VGD+V+ ++ +L V G + V R GGEEFA + + A +A +R+
Sbjct: 316 NDTYGHDVGDEVLRQVARRLRQTVRGLDL-VARYGGEEFAVVLPDTDLEAAIAIAERIRQ 374
Query: 202 IIENSQINIS-SGPSIHITISAGIAE-RCHKEPISTIIYRADQALYVAKKSGRNRVV 256
I S + +TIS G+AE + ++ I ++ RAD+ALY AK SGRNRVV
Sbjct: 375 KINELPFVHELSREPLEVTISIGVAEGKPGEDSIEELLKRADKALYKAKASGRNRVV 431
>gnl|CDD|34606 COG5001, COG5001, Predicted signal transduction protein containing
a membrane domain, an EAL and a GGDEF domain [Signal
transduction mechanisms].
Length = 663
Score = 83.5 bits (206), Expect = 5e-17
Identities = 50/165 (30%), Positives = 78/165 (47%), Gaps = 11/165 (6%)
Query: 103 LSRIDCLSGLLNHSAFISSL-------GSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVI 155
L+ +D L+GL N F + L +L + D+D FK +ND FGH GD+++
Sbjct: 227 LANLDSLTGLPNRRRFFAELDARLAAARQSGRRLVLGVIDLDGFKPVNDAFGHATGDRLL 286
Query: 156 AFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINIS-SGP 214
+ +L G P+ RLGG+EFA + ++ A+ R + E+ Q G
Sbjct: 287 IEVGRRLKAFDGAPILAARLGGDEFALII--PALEDDALRVAGARALCESLQAPYDLRGV 344
Query: 215 SIHITISAGIAE-RCHKEPISTIIYRADQALYVAKKSGRNRVVCF 258
+ + S GIA + + RAD ALY AK++G+ V F
Sbjct: 345 RVQVGASIGIAPFPSGADTSEQLFERADYALYHAKQNGKGAAVLF 389
>gnl|CDD|143637 cd07556, Nucleotidyl_cyc_III, Class III nucleotidyl cyclases.
Class III nucleotidyl cyclases are the largest, most
diverse group of nucleotidyl cyclases (NC's) containing
prokaryotic and eukaryotic proteins. They can be divided
into two major groups; the mononucleotidyl cyclases
(MNC's) and the diguanylate cyclases (DGC's). The
MNC's, which include the adenylate cyclases (AC's) and
the guanylate cyclases (GC's), have a conserved cyclase
homology domain (CHD), while the DGC's have a conserved
GGDEF domain, named after a conserved motif within this
subgroup. Their products, cyclic guanylyl and adenylyl
nucleotides, are second messengers that play important
roles in eukaryotic signal transduction and prokaryotic
sensory pathways.
Length = 133
Score = 50.4 bits (121), Expect = 5e-07
Identities = 23/127 (18%), Positives = 46/127 (36%), Gaps = 7/127 (5%)
Query: 129 LSIVFFDIDYFKQINDNFGHPVGDKVIA-FLSDQLVVVFGTPMFVGRLGGEEFAAAALGS 187
++I+F DI F + D G GD+++ ++ + + G+EF +
Sbjct: 2 VTILFADIVGFTSLADALGPDEGDELLNELAGRFDSLIRRSGDLKIKTIGDEFMVVSGLD 61
Query: 188 SEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAE------RCHKEPISTIIYRAD 241
A A D+R+ + + + + I I G R + ++ A
Sbjct: 62 HPAAAVAFAEDMREAVSALNQSEGNPVRVRIGIHTGPVVVGVIGSRPQYDVWGALVNLAS 121
Query: 242 QALYVAK 248
+ AK
Sbjct: 122 RMESQAK 128
>gnl|CDD|132878 cd07181, RNaseH_typeII_eukaryota_like, Eukaryotic Ribonuclease HII;
putative role in Okazaki fragment removal during
replication. Ribonuclease (RNase) HII
endonucleolytically hydrolyzes an RNA strand when it is
annealed to a complementary DNA strand in the presence
of divalent cations, in DNA replication and repair.
RNase H is classified into two families, type I
(prokaryotic RNase HI, eukaryotic RNase H1 and viral
RNase H) and type II (prokaryotic RNase HII and HIII,
and eukaryotic RNase H2/HII). The enzyme can be found in
bacteria, archaea, and eukaryotes. Most prokaryotic and
eukaryotic genomes contain multiple RNase H genes.
Despite a lack of evidence for homology from sequence
comparisons, type I and type II RNase H share a common
fold and similar steric configurations of the four
acidic active-site residues, suggesting identical or
very similar catalytic mechanisms. Eukaryotic RNase HII
is a type II RNase H that is active during replication
and is believed to play a role in removal of Okazaki
fragment primers and single ribonucleotides in DNA-DNA
duplexes. Eukaryotic RNase HII is functional when it
forms a complex with two other accessory proteins. It is
speculated that the two accessory subunits are required
for correct folding of the catalytic subunit of RNase
HII. It appears that type I and type II RNases H also
have overlapping functions in cells, as over-expression
of Escherichia coli RNase HII can complement an RNase HI
deletion phenotype in E. coli.
Length = 216
Score = 31.0 bits (71), Expect = 0.36
Identities = 15/62 (24%), Positives = 26/62 (41%), Gaps = 8/62 (12%)
Query: 84 YISGSILKELFISYNRISQLSRIDCLSGLLNHS-----AFISSLG---SYNEKLSIVFFD 135
YIS +L + N IS + I + +L+ ++ ++G Y KL +F
Sbjct: 71 YISAKMLARTKYNLNEISHDAAIGLIKSVLDKGVNVTEVYVDTVGPPEKYQAKLKKLFPG 130
Query: 136 ID 137
I
Sbjct: 131 IK 132
>gnl|CDD|35751 KOG0531, KOG0531, KOG0531, Protein phosphatase 1, regulatory
subunit, and related proteins [Signal transduction
mechanisms].
Length = 414
Score = 29.8 bits (66), Expect = 0.76
Identities = 19/89 (21%), Positives = 37/89 (41%), Gaps = 9/89 (10%)
Query: 55 LTPFYGLEYILVENLSLVIISITISLLLGYISGSILKELFISYNRISQLSRIDCLSGLLN 114
L+ LE + + + + I LL + L+ L +S+N+I++L + L+ L
Sbjct: 91 LSKLKSLEALDLYDNKIE----KIENLLSSLVN--LQVLDLSFNKITKLEGLSTLTLLKE 144
Query: 115 ---HSAFISSLGSYNEKLSIVFFDIDYFK 140
IS + S+ D+ Y +
Sbjct: 145 LNLSGNLISDISGLESLKSLKLLDLSYNR 173
>gnl|CDD|30108 cd01386, MYSc_type_XVIII, Myosin motor domain, type XVIII myosins.
This catalytic (head) domain has ATPase activity and
belongs to the larger group of P-loop NTPases. Myosins
are actin-dependent molecular motors that play important
roles in muscle contraction, cell motility, and
organelle transport. The head domain is a molecular
motor, which utilizes ATP hydrolysis to generate
directed movement toward the plus end along actin
filaments. A cyclical interaction between myosin and
actin provides the driving force. Rates of ATP
hydrolysis and consequently the speed of movement along
actin filaments vary widely, from about 0.04 micrometer
per second for myosin I to 4.5 micrometer per second for
myosin II in skeletal muscle. Myosin II moves in
discrete steps about 5-10 nm long and generates 1-5
piconewtons of force. Upon ATP binding, the myosin head
dissociates from an actin filament. ATP hydrolysis
causes the head to pivot and associate with a new actin
subunit. The release of Pi causes the head to pivot and
move the filament (power stroke). Release of ADP
completes the cycle..
Length = 767
Score = 29.2 bits (65), Expect = 1.2
Identities = 19/89 (21%), Positives = 30/89 (33%), Gaps = 14/89 (15%)
Query: 170 MFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCH 229
+F GR G A E SQ + SI T ++ A
Sbjct: 563 LFQGRAGLAPVCLGAGAGLEGT--------------SQQALRRSSSIRRTFTSSTAAVKR 608
Query: 230 KEPISTIIYRADQALYVAKKSGRNRVVCF 258
K P + + D + ++SG + V C+
Sbjct: 609 KSPCVQVKLQVDALIDTLRRSGLHFVHCY 637
>gnl|CDD|112616 pfam03812, KdgT, 2-keto-3-deoxygluconate permease.
Length = 314
Score = 28.6 bits (64), Expect = 1.6
Identities = 16/75 (21%), Positives = 34/75 (45%), Gaps = 2/75 (2%)
Query: 19 LESFSPHTFMIYFSIFFSIFIATVIFIANIFLFYIGLT-PFYGLEYILVENLSLVIISIT 77
+F+P YF F + I + I ++ F +G + F IL ++ +LV+ I
Sbjct: 25 CNTFAPGAGK-YFGSFTNGLITGTLPILAVWFFCMGASIDFRATGTILRKSGTLVVTKIA 83
Query: 78 ISLLLGYISGSILKE 92
+ ++ I+ + +
Sbjct: 84 FAWVVAVIAAQFIPD 98
>gnl|CDD|37725 KOG2514, KOG2514, KOG2514, Uncharacterized conserved protein
[Function unknown].
Length = 861
Score = 28.0 bits (62), Expect = 2.9
Identities = 18/78 (23%), Positives = 34/78 (43%), Gaps = 5/78 (6%)
Query: 17 KNLESFSPHTFMIYFSIFFSIFIATVIF-IANIFLFYIGLTPFYGLEYILVENLSLVIIS 75
L SFS FMI ++ FS + +++ I+ + F L + VII+
Sbjct: 385 AMLASFSFVLFMI--AVVFSAVLGVILYRISMVAALQ--CGKFTTSHAWLSATATAVIIN 440
Query: 76 ITISLLLGYISGSILKEL 93
+ + ++L I ++ L
Sbjct: 441 LVVIMILNAIYSNLASRL 458
>gnl|CDD|32455 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 27.5 bits (61), Expect = 4.4
Identities = 25/146 (17%), Positives = 54/146 (36%), Gaps = 19/146 (13%)
Query: 34 FFSIFIATVIFIANIFLFYIGLTPFYGLEYILVENLSLVIISITISLLLGYISGSILKEL 93
F + I T+I L ++ + Y + L+ V+ +I +++L+ I +L+
Sbjct: 266 FLTGSILTLIIDLLFALIFLAVMFLYSWKLTLI-----VLAAIPLNVLITLIFQPLLRRK 320
Query: 94 F---ISYNRISQLSRIDCLSGLL------NHSAFISSLGSYNEKLSIVFFDIDYFKQIND 144
I + Q ++ + G+ F S + K + F + I +
Sbjct: 321 TRKLIEESAEQQSFLVETIKGIETVKALAAEPRFRSQWDNRLAKQVNIGFKTEKLALILN 380
Query: 145 NFGHPVGDKVIAFLSDQLVVVFGTPM 170
++ LS L++ FG +
Sbjct: 381 TIK-----SLLQQLSSVLILWFGAIL 401
>gnl|CDD|143609 cd07585, nitrilase_7, Uncharacterized subgroup of the nitrilase
superfamily (putative class 13 nitrilases). The
nitrilase superfamily is comprised of nitrile- or
amide-hydrolyzing enzymes and amide-condensing enzymes,
which depend on a Glu-Lys-Cys catalytic triad. This
superfamily has been classified in the literature based
on global and structure based sequence analysis into
thirteen different enzyme classes (referred to as 1-13).
Class 13 represents proteins that at the time were
difficult to place in a distinct similarity group; this
subgroup represents either a new class or one that was
included previously in class 13. Members of this
superfamily generally form homomeric complexes, the
basic building block of which is a homodimer.
Length = 261
Score = 26.9 bits (60), Expect = 5.3
Identities = 8/35 (22%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 217 HITISAGIAERCHKEP-ISTIIYRADQALYVAKKS 250
+TI AG+ E+ P + ++ D ++ +K
Sbjct: 75 GLTILAGLIEKAGDRPYNTYLVCLPDGLVHRYRKL 109
>gnl|CDD|100006 cd02199, YjgF_YER057c_UK114_like_1, This group of proteins belong
to a large family of YjgF/YER057c/UK114-like proteins
present in bacteria, archaea, and eukaryotes with no
definitive function. The conserved domain is similar in
structure to chorismate mutase but there is no sequence
similarity and no functional connection. Members of this
family have been implicated in isoleucine (Yeo7, Ibm1,
aldR) and purine (YjgF) biosynthesis, as well as
threonine anaerobic degradation (tdcF) and mitochondrial
DNA maintenance (Ibm1). This domain homotrimerizes
forming a distinct intersubunit cavity that may serve as
a small molecule binding site..
Length = 142
Score = 26.7 bits (60), Expect = 6.6
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 5/42 (11%)
Query: 155 IAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILA 196
+ ++S QL V G ++ G++G + QEAA L
Sbjct: 25 LLYVSGQLPRVDGKLVYTGKVGADLSVEEG-----QEAARLC 61
>gnl|CDD|145484 pfam02361, CbiQ, Cobalt transport protein. This family consists of
various cobalt transport proteins Most of which are
found in Cobalamin (Vitamin B12) biosynthesis operons.
In Salmonella the cbiN cbiQ (product CbiQ in this
family) and cbiO are likely to form an active cobalt
transport system.
Length = 217
Score = 26.5 bits (59), Expect = 7.5
Identities = 16/102 (15%), Positives = 33/102 (32%), Gaps = 5/102 (4%)
Query: 21 SFSPHTFMIYFSIFFSIFIATVIFIANIFLFYIGLTPFYGLEYILVENLSLVIISITISL 80
++ + + ++ I+T + LF TP L L + ++ + L
Sbjct: 88 GIGITSWGLLRGLLLALRISTSLSAL---LFLALTTPPAELTSGLRRLGVPLELAEILLL 144
Query: 81 LLGYISGSILKELFISYNRISQLSRIDCLSGLLNHSAFISSL 122
YI +L E + + D G+ + L
Sbjct: 145 AYRYI--PLLLEEAQRIMQAQKSRGGDSKGGIRRRWRSLGLL 184
>gnl|CDD|177219 MTH00163, ND4, NADH dehydrogenase subunit 4; Provisional.
Length = 445
Score = 26.3 bits (59), Expect = 8.8
Identities = 14/68 (20%), Positives = 34/68 (50%), Gaps = 5/68 (7%)
Query: 27 FMIYFSIFFSIFIATVIFIANIFLFYIGLTPFYGLEYILVENLSLVIISITISLLLGYIS 86
+++ +F F+ ++F + + I F+GL+ + + L+++S I +L+ S
Sbjct: 22 WLVQSLLFLLSFLFMLLFSLSFYFSNISY--FFGLDLL---SFGLILLSFWICMLMILSS 76
Query: 87 GSILKELF 94
S+ K+
Sbjct: 77 ESVYKKNN 84
>gnl|CDD|32052 COG1867, TRM1, N2,N2-dimethylguanosine tRNA methyltransferase
[Translation, ribosomal structure and biogenesis].
Length = 380
Score = 26.0 bits (57), Expect = 9.8
Identities = 10/42 (23%), Positives = 17/42 (40%)
Query: 163 VVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIE 204
V P+++G L EEF L +E K+++
Sbjct: 266 KVHLAGPLWLGPLHDEEFIEEMLEIAEGLELGTKKRALKLLK 307
>gnl|CDD|145704 pfam02687, FtsX, Predicted permease. This is a family of predicted
permeases and hypothetical transmembrane proteins. The
lipoprotein-releasing system transmembrane protein lolC
from Buchnera aphidicola has been shown to transport
lipids targeted to the outer membrane across the inner
membrane. Both lolC and an ATP-binding cassette
transporter-like protein from Streptococcus cristatus
have been shown to require ATP.
Length = 174
Score = 26.2 bits (58), Expect = 9.8
Identities = 17/103 (16%), Positives = 37/103 (35%), Gaps = 13/103 (12%)
Query: 18 NLESFSPHTFMIYFSIFFSIFIATVIFIANIFLFYI-------------GLTPFYGLEYI 64
S ++ + + + ++ + N+ I G + + +
Sbjct: 41 LDLLLSNSIILLLSLLAVLLLLLALLILLNLLSISIAERRREIGILKALGASKKQIFKLL 100
Query: 65 LVENLSLVIISITISLLLGYISGSILKELFISYNRISQLSRID 107
L+E L L +I + LLLG++ +L ++ S ID
Sbjct: 101 LLEALLLGLIGSLLGLLLGFLLAYLLSSAIGYFSGFSLPLVID 143
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
0.326 0.142 0.409
Gapped
Lambda K H
0.267 0.0585 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,234,444
Number of extensions: 182585
Number of successful extensions: 1192
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1118
Number of HSP's successfully gapped: 199
Length of query: 266
Length of database: 6,263,737
Length adjustment: 92
Effective length of query: 174
Effective length of database: 4,275,709
Effective search space: 743973366
Effective search space used: 743973366
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 56 (25.7 bits)