RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2439
(146 letters)
>gnl|CDD|203730 pfam07700, HNOB, Heme NO binding. The HNOB (Heme NO Binding)
domain, is a predominantly alpha-helical domain and
binds heme via a covalent linkage to histidine. The HNOB
domain is predicted to function as a heme-dependent
sensor for gaseous ligands, and transduce diverse
downstream signals, in both bacteria and animals.
Length = 171
Score = 65.8 bits (161), Expect = 2e-14
Identities = 28/81 (34%), Positives = 44/81 (54%), Gaps = 7/81 (8%)
Query: 69 GIILAIAFQKL---EYGDDVWLKVLKKAGCKVS-CFNTHHIYPDIYMPDLATACASVIEG 124
GII + ++L +YG+DVW ++L+KAG + F H Y D + DL A + V+
Sbjct: 3 GIIFE-SLEELVQRKYGEDVWEQILEKAGFEPEGVFTVHESYDDSELYDLVAAASKVL-- 59
Query: 125 DLTSEYFMEFFGKCFVRYFSN 145
+ +E E FG+ F +FS
Sbjct: 60 GIPAEEIWEAFGRFFFTFFSE 80
Score = 64.6 bits (158), Expect = 6e-14
Identities = 25/69 (36%), Positives = 38/69 (55%), Gaps = 3/69 (4%)
Query: 2 EYGDDVWLKVLKKAGCKVS-CFNTHHIYPDIYMPDLATACASVIEGDLTSEYFMEFFGKC 60
+YG+DVW ++L+KAG + F H Y D + DL A + V+ + +E E FG+
Sbjct: 16 KYGEDVWEQILEKAGFEPEGVFTVHESYDDSELYDLVAAASKVL--GIPAEEIWEAFGRF 73
Query: 61 FVRYFSNLG 69
F +FS G
Sbjct: 74 FFTFFSESG 82
>gnl|CDD|177337 PHA02054, PHA02054, hypothetical protein.
Length = 94
Score = 28.1 bits (62), Expect = 0.69
Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 4/67 (5%)
Query: 36 LATACASVIEGDLTSEYFMEFFGKCFVRYFSNLGIILAIAFQKLEYGDDVWLKVLKKAGC 95
L A ++ + + EF + Y +++ + Q LEY D W GC
Sbjct: 10 LLVATVHLVSANPEVGSYDEFMQGAMIVYTNDIVHSKDNSVQFLEYLDTKW----GSVGC 65
Query: 96 KVSCFNT 102
+CF
Sbjct: 66 SDTCFQL 72
>gnl|CDD|235380 PRK05265, PRK05265, pyridoxine 5'-phosphate synthase; Provisional.
Length = 239
Score = 28.5 bits (65), Expect = 1.2
Identities = 14/35 (40%), Positives = 16/35 (45%), Gaps = 5/35 (14%)
Query: 12 LKKAGCKVSCFNTHHIYPDIYMPDLATAC-ASVIE 45
LK AG +VS F I PD + A A IE
Sbjct: 122 LKDAGIRVSLF----IDPDPEQIEAAAEVGADRIE 152
Score = 28.5 bits (65), Expect = 1.2
Identities = 14/35 (40%), Positives = 16/35 (45%), Gaps = 5/35 (14%)
Query: 90 LKKAGCKVSCFNTHHIYPDIYMPDLATAC-ASVIE 123
LK AG +VS F I PD + A A IE
Sbjct: 122 LKDAGIRVSLF----IDPDPEQIEAAAEVGADRIE 152
>gnl|CDD|224815 COG1903, CbiD, Cobalamin biosynthesis protein CbiD [Coenzyme
metabolism].
Length = 367
Score = 28.5 bits (64), Expect = 1.3
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 10 KVLKKAGCKVSCFNTHHIYPDIYMPDLATACA 41
K++K A FNTH D + LA A A
Sbjct: 259 KLIKLAA---GIFNTHSRVADARLEILAAAAA 287
Score = 28.5 bits (64), Expect = 1.3
Identities = 12/32 (37%), Positives = 15/32 (46%), Gaps = 3/32 (9%)
Query: 88 KVLKKAGCKVSCFNTHHIYPDIYMPDLATACA 119
K++K A FNTH D + LA A A
Sbjct: 259 KLIKLAA---GIFNTHSRVADARLEILAAAAA 287
>gnl|CDD|234615 PRK00075, cbiD, cobalt-precorrin-6A synthase; Reviewed.
Length = 361
Score = 28.3 bits (64), Expect = 1.6
Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 12/56 (21%)
Query: 10 KVLKKAGCKVSCFNTHHIYPDIYMPDLATACASV---------IEGDLTSEYFMEF 56
K++K A F+TH D + LA A I T+E +E
Sbjct: 257 KLIKLAA---GIFHTHSHVADARLEILAALAALAGAPLELLEKILAANTTEEALEL 309
Score = 28.3 bits (64), Expect = 1.6
Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 12/56 (21%)
Query: 88 KVLKKAGCKVSCFNTHHIYPDIYMPDLATACASV---------IEGDLTSEYFMEF 134
K++K A F+TH D + LA A I T+E +E
Sbjct: 257 KLIKLAA---GIFHTHSHVADARLEILAALAALAGAPLELLEKILAANTTEEALEL 309
>gnl|CDD|215549 PLN03044, PLN03044, GTP cyclohydrolase I; Provisional.
Length = 188
Score = 27.5 bits (61), Expect = 2.0
Identities = 9/28 (32%), Positives = 14/28 (50%)
Query: 48 LTSEYFMEFFGKCFVRYFSNLGIILAIA 75
E + F G+ V Y N G+IL ++
Sbjct: 75 TCEETMVPFTGRIHVGYIPNAGVILGLS 102
>gnl|CDD|128420 smart00110, C1Q, Complement component C1q domain. Globular domain
found in many collagens and eponymously in complement
C1q. When part of full length proteins these domains
form a 'bouquet' due to the multimerization of
heterotrimers. The C1q fold is similar to that of tumour
necrosis factor.
Length = 135
Score = 26.9 bits (60), Expect = 2.7
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 6/37 (16%)
Query: 78 KLEYGDDVWLKVLKKAG------CKVSCFNTHHIYPD 108
+L GD VWL++ + S F+ ++PD
Sbjct: 99 QLRQGDQVWLELPDEKNGLYAGEYVDSTFSGFLLFPD 135
Score = 26.5 bits (59), Expect = 3.6
Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 6/36 (16%)
Query: 1 LEYGDDVWLKVLKKAG------CKVSCFNTHHIYPD 30
L GD VWL++ + S F+ ++PD
Sbjct: 100 LRQGDQVWLELPDEKNGLYAGEYVDSTFSGFLLFPD 135
>gnl|CDD|215834 pfam00275, EPSP_synthase, EPSP synthase (3-phosphoshikimate
1-carboxyvinyltransferase).
Length = 415
Score = 27.2 bits (61), Expect = 3.0
Identities = 22/94 (23%), Positives = 33/94 (35%), Gaps = 16/94 (17%)
Query: 9 LKVLKKAGCKVSCFNTHHIYPDIYMPDLATACASVIEGDLTSE-YFMEFF----GKCFVR 63
+L K G K+ T I +EGD +S YF+ G V
Sbjct: 198 ENMLNKFGAKIEGSGTETSI-YIKGGQKLPGVEYRVEGDRSSAAYFLAAAAITGGTVKVE 256
Query: 64 YFSNLGIILAIAFQKLEYGDDVWLKVLKKAGCKV 97
N+GI GD ++L+K G ++
Sbjct: 257 ---NVGI-------NSLQGDRAADEILEKMGAEI 280
>gnl|CDD|233467 TIGR01554, major_cap_HK97, phage major capsid protein, HK97 family.
This model family represents the major capsid protein
component of the heads (capsids) of bacteriophage HK97,
phi-105, P27, and related phage. This model represents
one of several analogous families lacking detectable
sequence similarity. The gene encoding this component is
typically located in an operon encoding the small and
large terminase subunits, the portal protein and the
prohead or maturation protease [Mobile and
extrachromosomal element functions, Prophage functions].
Length = 384
Score = 27.3 bits (61), Expect = 3.6
Identities = 7/28 (25%), Positives = 13/28 (46%)
Query: 27 IYPDIYMPDLATACASVIEGDLTSEYFM 54
+ MPD+A ++ GD + Y +
Sbjct: 313 VVETEDMPDVAAGAKPILFGDFSRGYLI 340
Score = 27.3 bits (61), Expect = 3.6
Identities = 7/28 (25%), Positives = 13/28 (46%)
Query: 105 IYPDIYMPDLATACASVIEGDLTSEYFM 132
+ MPD+A ++ GD + Y +
Sbjct: 313 VVETEDMPDVAAGAKPILFGDFSRGYLI 340
>gnl|CDD|237525 PRK13830, PRK13830, conjugal transfer protein TrbE; Provisional.
Length = 818
Score = 27.1 bits (60), Expect = 3.7
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 8 WLKVLKKAGCKV 19
WLKVL+KA C V
Sbjct: 677 WLKVLRKANCAV 688
Score = 27.1 bits (60), Expect = 3.7
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 86 WLKVLKKAGCKV 97
WLKVL+KA C V
Sbjct: 677 WLKVLRKANCAV 688
>gnl|CDD|224194 COG1275, TehA, Tellurite resistance protein and related permeases
[Inorganic ion transport and metabolism].
Length = 329
Score = 26.9 bits (60), Expect = 4.5
Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 3/58 (5%)
Query: 22 FNTHHIYPDIYMPDLATACASVIEGDLTSEYFME---FFGKCFVRYFSNLGIILAIAF 76
F I P ++P + AS+ L YF+ FFG F Y I+L F
Sbjct: 134 FELETITPSWFLPPVGIIVASLTASVLLGAYFVIGYVFFGAGFFSYLVLFPIVLYRLF 191
>gnl|CDD|197252 cd09155, PLDc_PaCLS_like_1, Putative catalytic domain, repeat 1,
of Pseudomonas aeruginosa cardiolipin synthase and
similar proteins. Putative catalytic domain, repeat 1,
of Pseudomonas aeruginosa cardiolipin (CL) synthase
(PaCLS) and similar proteins. Although PaCLS and
similar proteins have not been functionally
characterized, members in this subfamily show high
sequence homology to bacterial CL synthases, which
catalyze the reversible phosphatidyl group transfer
between two phosphatidylglycerol molecules to form CL
and glycerol. Moreover, PaCLS and other members of this
subfamily contain two HKD motifs (H-x-K-x(4)-D, where x
represents any amino acid residue) that characterizes
the phospholipase D (PLD) superfamily. The two motifs
may be part of the active site and may be involved in
phosphatidyl group transfer.
Length = 156
Score = 26.1 bits (58), Expect = 5.7
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 8 WLKVLKKAGCKVSCFNTHH 26
+++ L+KAG +VS FNT
Sbjct: 67 YIERLRKAGVEVSAFNTTR 85
Score = 26.1 bits (58), Expect = 5.7
Identities = 9/19 (47%), Positives = 14/19 (73%)
Query: 86 WLKVLKKAGCKVSCFNTHH 104
+++ L+KAG +VS FNT
Sbjct: 67 YIERLRKAGVEVSAFNTTR 85
>gnl|CDD|187564 cd05254, dTDP_HR_like_SDR_e, dTDP-6-deoxy-L-lyxo-4-hexulose
reductase and related proteins, extended (e) SDRs.
dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended
SDR, synthesizes dTDP-L-rhamnose from
alpha-D-glucose-1-phosphate, providing the precursor of
L-rhamnose, an essential cell wall component of many
pathogenic bacteria. This subgroup has the
characteristic active site tetrad and NADP-binding
motif. This subgroup also contains human MAT2B, the
regulatory subunit of methionine adenosyltransferase
(MAT); MAT catalyzes S-adenosylmethionine synthesis. The
human gene encoding MAT2B encodes two major splicing
variants which are induced in human cell liver cancer
and regulate HuR, an mRNA-binding protein which
stabilizes the mRNA of several cyclins, to affect cell
proliferation. Both MAT2B variants include this extended
SDR domain. Extended SDRs are distinct from classical
SDRs. In addition to the Rossmann fold (alpha/beta
folding pattern with a central beta-sheet) core region
typical of all SDRs, extended SDRs have a less conserved
C-terminal extension of approximately 100 amino acids.
Extended SDRs are a diverse collection of proteins, and
include isomerases, epimerases, oxidoreductases, and
lyases; they typically have a TGXXGXXG cofactor binding
motif. SDRs are a functionally diverse family of
oxidoreductases that have a single domain with a
structurally conserved Rossmann fold, an
NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Sequence identity between different
SDR enzymes is typically in the 15-30% range; they
catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. Atypical SDRs
generally lack the catalytic residues characteristic of
the SDRs, and their glycine-rich NAD(P)-binding motif is
often different from the forms normally seen in
classical or extended SDRs. Complex (multidomain) SDRs
such as ketoreductase domains of fatty acid synthase
have a GGXGXXG NAD(P)-binding motif and an altered
active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 280
Score = 26.1 bits (58), Expect = 7.0
Identities = 16/67 (23%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 61 FVRYFSNLGIIL--AIAFQKLEYGDDVWLKVLKKA--GCKVSCFNTHHIYPDIYMPDLAT 116
V + +IL + + +L+ G++ +L+ A +V+ + P Y DLA
Sbjct: 138 AVLNANPRYLILRTSWLYGELKNGENFVEWMLRLAAERKEVNVVHDQIGSP-TYAADLAD 196
Query: 117 ACASVIE 123
A +IE
Sbjct: 197 AILELIE 203
>gnl|CDD|217741 pfam03806, ABG_transport, AbgT putative transporter family.
Length = 502
Score = 26.2 bits (58), Expect = 7.8
Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 2/23 (8%)
Query: 54 MEFFGKCFVRYF--SNLGIILAI 74
+ FF FV F SN+G ILA+
Sbjct: 344 IAFFAAQFVAMFNWSNMGPILAV 366
>gnl|CDD|213991 cd07436, PHP_PolX, Polymerase and Histidinol Phosphatase domain of
bacterial polymerase X. The bacterial/archaeal X-family
DNA polymerases (PolXs) have a PHP domain at their
C-terminus. The bacterial/archaeal PolX core domain and
PHP domain interact with each other and together are
involved in metal dependent 3'-5' exonuclease activity.
The PHP (also called histidinol phosphatase-2/HIS2)
domain is associated with several types of DNA
polymerases, such as PolIIIA and family X DNA
polymerases, stand alone histidinol phosphate
phosphatases (HisPPases), and a number of
uncharacterized protein families. The PHP domain has
four conserved sequence motifs and contains an invariant
histidine that is involved in metal ion coordination.
PolX is found in all kingdoms, however bacterial PolXs
have a completely different domain structure from
eukaryotic PolXs. Bacterial PolX has an extended
conformation in contrast to the common closed 'right
hand' conformation for DNA polymerases. This extended
conformation is stabilized by the PHP domain. The PHP
domain of PolX is structurally homologous to other
members of the PHP family that has a distorted
(beta/alpha)7 barrel fold with a trinuclear metal site
on the C-terminal side of the barrel.
Length = 237
Score = 25.8 bits (58), Expect = 9.9
Identities = 9/25 (36%), Positives = 13/25 (52%), Gaps = 3/25 (12%)
Query: 5 DDVWLKVLKKAGCKVSCFNT--HHI 27
DD + K+AG K++ NT H
Sbjct: 178 DDRHARRAKEAGVKIAI-NTDAHST 201
Score = 25.8 bits (58), Expect = 9.9
Identities = 9/25 (36%), Positives = 13/25 (52%), Gaps = 3/25 (12%)
Query: 83 DDVWLKVLKKAGCKVSCFNT--HHI 105
DD + K+AG K++ NT H
Sbjct: 178 DDRHARRAKEAGVKIAI-NTDAHST 201
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
0.329 0.144 0.472
Gapped
Lambda K H
0.267 0.0733 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,491,512
Number of extensions: 656185
Number of successful extensions: 917
Number of sequences better than 10.0: 1
Number of HSP's gapped: 913
Number of HSP's successfully gapped: 36
Length of query: 146
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 58
Effective length of database: 7,034,450
Effective search space: 407998100
Effective search space used: 407998100
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 (21.8 bits)
S2: 54 (24.6 bits)