RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13822
(123 letters)
>gnl|CDD|214485 smart00044, CYCc, Adenylyl- / guanylyl cyclase, catalytic domain.
Present in two copies in mammalian adenylyl cyclases.
Eubacterial homologues are known. Two residues (Asn,
Arg) are thought to be involved in catalysis. These
cyclases have important roles in a diverse range of
cellular processes.
Length = 194
Score = 155 bits (394), Expect = 2e-49
Identities = 60/116 (51%), Positives = 78/116 (67%), Gaps = 2/116 (1%)
Query: 2 PVDPEDFREVTIYFSDIVGFTTISAYSTPFEVVDLLNDLYTCFDATINAYNVYKVETIGD 61
PV E + VTI FSDIVGFT++ + STP +VV+LLNDLY+ FD I+ + YKV+TIGD
Sbjct: 28 PVPAESYDNVTILFSDIVGFTSLCSTSTPEQVVNLLNDLYSRFDQIIDRHGGYKVKTIGD 87
Query: 62 AYMVVGGLPVR-IPDHADQIATMALDLLHHSGRFKIRHLPYTPLRLRIGLHTGRPV 116
AYMV GLP + DHA+ IA ALD++ ++H LR+RIG+HTG V
Sbjct: 88 AYMVASGLPEEALVDHAELIADEALDMVEELKTVLVQH-REEGLRVRIGIHTGPVV 142
>gnl|CDD|201086 pfam00211, Guanylate_cyc, Adenylate and Guanylate cyclase catalytic
domain.
Length = 184
Score = 147 bits (373), Expect = 3e-46
Identities = 56/115 (48%), Positives = 73/115 (63%), Gaps = 2/115 (1%)
Query: 3 VDPEDFREVTIYFSDIVGFTTISAYSTPFEVVDLLNDLYTCFDATINAYNVYKVETIGDA 62
V + + VTI F+DIVGFT +S+ +P E+V LLNDLYT FD ++ + VYKV+TIGDA
Sbjct: 1 VYAQSYDNVTILFADIVGFTALSSRHSPEELVRLLNDLYTRFDELLDKHGVYKVKTIGDA 60
Query: 63 YMVVGGLPVRIPDHADQIATMALDLLHHSGRFKIRHLPYTPLRLRIGLHTGRPVS 117
YM GLP P HA +A MALD+L I LR+R+G+HTG V+
Sbjct: 61 YMAASGLPEPSPAHAQTLAEMALDMLEAIKSVNIHSFE--GLRVRVGIHTGPVVA 113
>gnl|CDD|143636 cd07302, CHD, cyclase homology domain. Catalytic domains of the
mononucleotidyl cyclases (MNC's), also called cyclase
homology domains (CHDs), are part of the class III
nucleotidyl cyclases. This class includes eukaryotic and
prokaryotic adenylate cyclases (AC's) and guanylate
cyclases (GC's). They seem to share a common catalytic
mechanism in their requirement for two magnesium ions to
bind the polyphosphate moiety of the nucleotide.
Length = 177
Score = 131 bits (331), Expect = 4e-40
Identities = 46/107 (42%), Positives = 61/107 (57%)
Query: 10 EVTIYFSDIVGFTTISAYSTPFEVVDLLNDLYTCFDATINAYNVYKVETIGDAYMVVGGL 69
EVT+ F+DIVGFT +S P E+V+LLN+ ++ FD I + +TIGDA M V GL
Sbjct: 1 EVTVLFADIVGFTALSERLGPEELVELLNEYFSAFDEIIERHGGTVDKTIGDAVMAVFGL 60
Query: 70 PVRIPDHADQIATMALDLLHHSGRFKIRHLPYTPLRLRIGLHTGRPV 116
P DHA++ AL++ PLRLRIG+HTG V
Sbjct: 61 PGAHEDHAERAVRAALEMQEALAELNAEREGGPPLRLRIGIHTGPVV 107
>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 = 87.0 bits (216), Expect = 3e-23
Identities = 41/108 (37%), Positives = 56/108 (51%), Gaps = 7/108 (6%)
Query: 10 EVTIYFSDIVGFTTISAYSTPFEVVDLLNDLYTCFDATINAYNVYKVETIGDAYMVVGGL 69
VTI F+DIVGFT+++ P E +LLN+L FD+ I K++TIGD +MVV G
Sbjct: 1 PVTILFADIVGFTSLADALGPDEGDELLNELAGRFDSLIRRSGDLKIKTIGDEFMVVSG- 59
Query: 70 PVRIPDHADQIATMALDLLHHSGRFKIRHLPYTPLRLRIGLHTGRPVS 117
DH A D+ + P+R+RIG+HTG V
Sbjct: 60 ----LDHPAAAVAFAEDMREAVSA--LNQSEGNPVRVRIGIHTGPVVV 101
>gnl|CDD|225025 COG2114, CyaA, Adenylate cyclase, family 3 (some proteins contain
HAMP domain) [Signal transduction mechanisms].
Length = 227
Score = 84.5 bits (209), Expect = 2e-21
Identities = 35/114 (30%), Positives = 51/114 (44%), Gaps = 5/114 (4%)
Query: 4 DPEDFREVTIYFSDIVGFTTISAYSTPFEVVDLLNDLYTCFDATINAYNVYKVETIGDAY 63
R VT+ F+DIVG T +S +V+LLN + + + V+ IGD +
Sbjct: 40 GGAGDRRVTLLFADIVGSTELSESLGDEALVELLNLYFDAVAEVVARHGGRVVKFIGDGF 99
Query: 64 MVVGGLPVRIPDHADQIATMALDLLHHSGRFKIRHLPYTPLRLRIGLHTGRPVS 117
+ V G P + D + L L + R L LR+RIG+HTG V
Sbjct: 100 LAVFGRPSPLEDAVACALDLQLALRNPLAR-----LRRESLRVRIGIHTGEVVV 148
>gnl|CDD|234389 TIGR03903, TOMM_kin_cyc, TOMM system kinase/cyclase fusion protein.
This model represents proteins of 1350 in length, in
multiple species of Burkholderia, in Acidovorax avenae
subsp. citrulli AAC00-1 and Delftia acidovorans SPH-1,
and in multiple copies in Sorangium cellulosum, in
genomic neighborhoods that include a
cyclodehydratase/docking scaffold fusion protein
(TIGR03882) and a member of the thiazole/oxazole
modified metabolite (TOMM) precursor family TIGR03795.
It has a kinase domain in the N-terminal 300 amino
acids, followed by a cyclase homology domain, followed
by regions without named domain definitions. It is a
probable bacteriocin-like metabolite biosynthesis
protein [Cellular processes, Toxin production and
resistance].
Length = 1266
Score = 29.0 bits (65), Expect = 0.63
Identities = 16/58 (27%), Positives = 25/58 (43%), Gaps = 2/58 (3%)
Query: 58 TIGDAYMVVGGLPVRIPDHADQIATMALDLLHHSGRFKIRHLPYTPLRLRI--GLHTG 113
+GD + G P A + A AL+++ +GR R+ I G+HTG
Sbjct: 338 VLGDTLLFYFGYPSAAERDARRAARAALEMVRQAGRKGEAAAGEGKWRVEIAAGIHTG 395
>gnl|CDD|225593 COG3051, CitF, Citrate lyase, alpha subunit [Energy production and
conversion].
Length = 513
Score = 27.8 bits (62), Expect = 1.7
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 53 VYKVETIGDAYMVVGGLPVRIPDHADQ--IATMALDLLHHSGRFK 95
V +V+ +GD + G R+ + + IA A D++ +SG FK
Sbjct: 229 VVQVDAVGDPKKIGAG-ATRMTTNPRELLIARSAADVIVNSGYFK 272
>gnl|CDD|132552 TIGR03513, GldL_gliding, gliding motility-associated protein GldL.
This protein family, GldL, is named for the member from
Flavobacterium johnsoniae, which is required for a type
of rapid gliding motility found in certain members of
the Bacteriodetes. However, members are found also in
several members of the Bacteriodetes that appear not to
be motile [Cellular processes, Chemotaxis and motility].
Length = 202
Score = 26.8 bits (59), Expect = 3.3
Identities = 9/19 (47%), Positives = 10/19 (52%)
Query: 94 FKIRHLPYTPLRLRIGLHT 112
FKI H P L +GL T
Sbjct: 21 FKIMHWPMGNPMLFVGLIT 39
>gnl|CDD|220083 pfam08973, TM1506, Domain of unknown function (DUF1893). A
member of the deaminase fold that binds an unknown
ligand in the crystal structure. The protein is
ADP-ribosylated at a conserved aspartate. Contextual
analysis suggests that the domain is likely to bind NAD
or ADP ribose either to sense redox states or to
function as a regulatory ADP ribosyltransferase.
Length = 134
Score = 26.2 bits (58), Expect = 3.7
Identities = 22/60 (36%), Positives = 30/60 (50%), Gaps = 9/60 (15%)
Query: 37 LNDLYTCFDATINAYNVY-KVETIGDA---YMVVGGLPVRIPDHADQIATMALDLLHHSG 92
L DL T + + KV IG A MV+GG+ +AD I+ ALDLL ++G
Sbjct: 34 LYDLLTDEPEFLEGALIADKV--IGKAAAALMVLGGIKEV---YADIISEPALDLLENAG 88
>gnl|CDD|225000 COG2089, SpsE, Sialic acid synthase [Cell envelope biogenesis,
outer membrane].
Length = 347
Score = 26.1 bits (58), Expect = 5.5
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 17 DIVGFTTISAYSTPFEVVDL--LNDLYTCFDATI 48
DI SAY PFE V+L + L F+A +
Sbjct: 176 DIALLHCTSAYPAPFEDVNLKAIPKLAEAFNAIV 209
>gnl|CDD|226815 COG4380, COG4380, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 216
Score = 25.6 bits (56), Expect = 6.6
Identities = 9/33 (27%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 3 VDPEDFREVTIYFSDIVGFTTISAYSTPFEVVD 35
V P + I+ +D V + T++ Y T ++++D
Sbjct: 94 VRPAKLHQ--IFGADAVLYITVTEYGTSYQIID 124
>gnl|CDD|237294 PRK13186, lpxC, UDP-3-O-[3-hydroxymyristoyl] N-acetylglucosamine
deacetylase; Reviewed.
Length = 295
Score = 25.5 bits (57), Expect = 7.9
Identities = 7/14 (50%), Positives = 11/14 (78%)
Query: 108 IGLHTGRPVSKHLR 121
+GLH+G+ V+ LR
Sbjct: 16 VGLHSGKKVTLTLR 29
>gnl|CDD|235050 PRK02546, PRK02546, NAD(P)H-quinone oxidoreductase subunit 4;
Provisional.
Length = 525
Score = 25.8 bits (57), Expect = 8.4
Identities = 10/16 (62%), Positives = 11/16 (68%)
Query: 19 VGFTTISAYSTPFEVV 34
VGF T AY+ PF VV
Sbjct: 404 VGFATSDAYTLPFRVV 419
>gnl|CDD|181319 PRK08246, PRK08246, threonine dehydratase; Provisional.
Length = 310
Score = 25.3 bits (56), Expect = 8.8
Identities = 8/29 (27%), Positives = 11/29 (37%)
Query: 69 LPVRIPDHADQIATMALDLLHHSGRFKIR 97
L + L+ L H+G FK R
Sbjct: 27 LEADGAGFGPAPVWLKLEHLQHTGSFKAR 55
>gnl|CDD|130646 TIGR01584, citF, citrate lyase, alpha subunit. This is a model of
the alpha subunit of the holoenzyme citrate lyase (EC
4.1.3.6) composed of alpha (EC 2.8.3.10), beta (EC
4.1.3.34), and acyl carrier protein subunits in a
stoichiometric relationship of 6:6:6. Citrate lyase is
an enzyme which converts citrate to oxaloacetate. In
bacteria, this reaction is involved in citrate
fermentation. The alpha subunit catalyzes the reaction
Acetyl-CoA + citrate = acetate + (3S)-citryl-CoA. The
seed contains an experimentally characterized member
from Lactococcus lactis subsp. lactis. The model covers
both Gram positive and Gram negative bacteria. It is
quite robust with queries scoring either quite well or
quite poorly against the model. There are currently no
hits in between the noise cutoff and trusted cutoff
[Energy metabolism, Fermentation].
Length = 492
Score = 25.6 bits (56), Expect = 9.2
Identities = 16/45 (35%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 53 VYKVETIGDAYMVVGGLPVRIPDHADQ--IATMALDLLHHSGRFK 95
V KV+ +GD + G R + IA MA D++ +SG FK
Sbjct: 207 VVKVDAVGDPKKIGSG-ATRFTKDPKELLIAKMANDVIVNSGYFK 250
>gnl|CDD|218198 pfam04662, Luteo_PO, Luteovirus P0 protein. This family of
proteins may be involved in suppression of PTGS a plant
defence mechanism.
Length = 208
Score = 25.4 bits (56), Expect = 9.2
Identities = 6/27 (22%), Positives = 8/27 (29%)
Query: 89 HHSGRFKIRHLPYTPLRLRIGLHTGRP 115
++ Y R GL G P
Sbjct: 61 RYTPGGLQLPRSYHEDLARFGLACGYP 87
>gnl|CDD|205122 pfam12875, DUF3826, Protein of unknown function (DUF3826). This is
a putative sugar-binding family.
Length = 187
Score = 25.1 bits (55), Expect = 9.5
Identities = 14/50 (28%), Positives = 22/50 (44%), Gaps = 5/50 (10%)
Query: 38 NDLYTC---FDATINAY-NVYKVETIGDAYMVVGGLPVRIPDHADQIATM 83
LY F A ++ Y ++E + D M G LPV + D I ++
Sbjct: 76 AALYRLHFAFPADLSLYLTEEQIEAVKDG-MTYGVLPVTYKAYQDMIPSL 124
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
0.325 0.143 0.434
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,677,728
Number of extensions: 590224
Number of successful extensions: 677
Number of sequences better than 10.0: 1
Number of HSP's gapped: 671
Number of HSP's successfully gapped: 23
Length of query: 123
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 38
Effective length of database: 7,167,512
Effective search space: 272365456
Effective search space used: 272365456
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.1 bits)