RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781188|ref|YP_003065601.1| hypothetical protein
CLIBASIA_05475 [Candidatus Liberibacter asiaticus str. psy62]
(185 letters)
>gnl|CDD|132367 TIGR03324, alt_F1F0_F1_al, alternate F1F0 ATPase, F1 subunit alpha.
A small number of taxonomically diverse prokaryotic
species, including Methanosarcina barkeri, have what
appears to be a second ATP synthase, in addition to the
normal F1F0 ATPase in bacteria and A1A0 ATPase in
archaea. These enzymes use ion gradients to synthesize
ATP, and in principle may run in either direction. This
model represents the F1 alpha subunit of this apparent
second ATP synthase.
Length = 497
Score = 33.2 bits (76), Expect = 0.044
Identities = 27/76 (35%), Positives = 35/76 (46%), Gaps = 11/76 (14%)
Query: 17 GCIYYSPELFA-GILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQ-- 73
G IY SP LF G+L V GK++ V K + YR + DLKL A E L+
Sbjct: 340 GQIYLSPTLFELGVLPAVDVGKSVSRVGGKAQLAA----YRAVAGDLKLAYAQFEELETF 395
Query: 74 ----CRLDLLAEELLE 85
RLD + +E
Sbjct: 396 ARFGARLDENTRKTIE 411
>gnl|CDD|162209 TIGR01116, ATPase-IIA1_Ca, sarco/endoplasmic reticulum
calcium-translocating P-type ATPase. The calcium P-type
ATPases have been characterized as Type IIA based on a
phylogenetic analysis which distinguishes this group
from the Type IIB PMCA calcium pump modelled by
TIGR01517. A separate analysis divides Type IIA into
sub-types, SERCA and PMR1, the latter of which is
modelled by TIGR01522.
Length = 917
Score = 31.3 bits (71), Expect = 0.15
Identities = 23/59 (38%), Positives = 30/59 (50%), Gaps = 6/59 (10%)
Query: 25 LFAGILDQVANGKALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEALQCRLDLLAEEL 83
LF+G L V GKA G V+R GM ST I+ +++ E LQ +LD E L
Sbjct: 152 LFSGTL--VVAGKARGVVVR-TGM---STEIGKIRDEMRAAEQEDTPLQKKLDEFGELL 204
>gnl|CDD|185239 PRK15339, PRK15339, type III secretion system outer membrane pore
InvG; Provisional.
Length = 559
Score = 29.4 bits (66), Expect = 0.66
Identities = 17/35 (48%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 94 LANPVFYSKMRDRKQRMGTF-------LLEKLSNQ 121
L PV SK+ RKQ G F LLEKLS Q
Sbjct: 52 LKKPVIVSKLAARKQISGNFDLHDPNALLEKLSLQ 86
>gnl|CDD|132422 TIGR03379, glycerol3P_GlpC, glycerol-3-phosphate dehydrogenase,
anaerobic, C subunit. Members of this protein family
are the membrane-anchoring, non-catalytic C subunit,
product of the glpC gene, of a three-subunit,
FAD-dependent, anaerobic glycerol-3-phosphate
dehydrogenase. GlpC lasks classical hydrophobic
transmembrane helices; Cole, et al suggest interaction
with the membrane may involve amphipathic helices. GlcC
has conserved Cys-containing motifs suggestive of
iron-sulfur binding. This complex is found mostly in
Escherichia coli and closely related species.
Length = 397
Score = 28.2 bits (63), Expect = 1.4
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 9/55 (16%)
Query: 25 LFAGILDQVANGKALGHVLRKV-------GMPKYS--TFYRWIKKDLKLQEAYTE 70
FA I++ + K + +L K +PKYS TF RW KK+ Q Y
Sbjct: 108 PFAPIVNAITGLKPVKKLLDKTLGVSKHRTLPKYSFGTFRRWYKKNATSQALYER 162
>gnl|CDD|183057 PRK11249, katE, hydroperoxidase II; Provisional.
Length = 752
Score = 26.9 bits (60), Expect = 2.8
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 144 LREHYKHLKPI 154
L E YKHLKPI
Sbjct: 684 LLEAYKHLKPI 694
>gnl|CDD|149086 pfam07820, TraC, TraC-like protein. The members of this family are
sequences that are similar to TraC. The gene encoding
this protein is one of a group of genes found on plasmid
p42a of Rhizobium etli CFN42 that are thought to be
involved in the process of plasmid self-transmission.
Mobilisation of plasmid p42a is of importance as it is
required for transfer of plasmid p42a, which is also
known as plasmid pSym as it carries most of the genes
required for nodulation and nitrogen fixation by the
symbiotic bacterium. The predicted protein products of
p42a are similar to known transfer proteins of
Agrobacterium tumefaciens plasmid pTiC58.
Length = 92
Score = 26.6 bits (59), Expect = 3.5
Identities = 15/55 (27%), Positives = 26/55 (47%), Gaps = 5/55 (9%)
Query: 132 KHTIDLRPAIERLREHYKHLKPIDSERIPHKSTEKPL---EIVESSIAEQSIIEH 183
K + +R I +L+E K + ++ERI + + L EI E + Q+ E
Sbjct: 2 KPSSKIREEIAKLQEQLKQAETREAERIGRIALKAGLGEIEIEEEEL--QAAFEE 54
>gnl|CDD|183822 PRK12900, secA, preprotein translocase subunit SecA; Reviewed.
Length = 1025
Score = 26.7 bits (59), Expect = 4.2
Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 9/56 (16%)
Query: 131 SKHTID---LRPAIERLREHYKHLKPIDSERIPHKSTE------KPLEIVESSIAE 177
SKH D ++P I+R+ E L + + + K E LE +E +
Sbjct: 11 SKHEKDIKKIQPIIDRINEIQASLASLSDDALREKGMELKSRVRGALEPIEQKKKD 66
>gnl|CDD|178622 PLN03073, PLN03073, ABC transporter F family; Provisional.
Length = 718
Score = 26.4 bits (58), Expect = 4.4
Identities = 26/90 (28%), Positives = 35/90 (38%), Gaps = 23/90 (25%)
Query: 69 TEALQCRLDLLAE--ELLEEPAPTAEELANPVFYSKMRDRKQRMGTFLLEKLSNQKYGPR 126
T ALQC L+ E +LLEE A +QR F E +
Sbjct: 249 TTALQCVLNTDIERTQLLEEEAQLVA--------------QQRELEFETETGKGK----- 289
Query: 127 VSVESKHTIDLRPAIERLREHYKHLKPIDS 156
+K +D +RL E YK L+ ID+
Sbjct: 290 --GANKDGVDKDAVSQRLEEIYKRLELIDA 317
>gnl|CDD|184034 PRK13405, bchH, magnesium chelatase subunit H; Provisional.
Length = 1209
Score = 25.8 bits (57), Expect = 6.6
Identities = 6/13 (46%), Positives = 10/13 (76%)
Query: 51 YSTFYRWIKKDLK 63
+S FYRW+++D
Sbjct: 584 FSAFYRWLREDFG 596
>gnl|CDD|177911 PLN02271, PLN02271, serine hydroxymethyltransferase.
Length = 586
Score = 25.5 bits (56), Expect = 7.6
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 6/42 (14%)
Query: 38 ALGHVLRKVGMPKYSTFYRWIKKDLKLQEAYTEAL---QCRL 76
AL L++V P+Y + + +KK+ + A AL +CRL
Sbjct: 420 ALAIALKQVATPEYKAYMQQVKKNAQ---ALASALLRRKCRL 458
>gnl|CDD|183283 PRK11706, PRK11706, TDP-4-oxo-6-deoxy-D-glucose transaminase;
Provisional.
Length = 375
Score = 25.6 bits (57), Expect = 8.0
Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 6/61 (9%)
Query: 62 LKLQEAYTEALQCRLDLLAEELLEEPAPTAEELANP-VFYSKMRDRKQRMGTFLLEKLSN 120
L L + Y +AL L +E P+ + N +FY K+RD + R + L+ L
Sbjct: 257 LALWQRYYDALA---PLAEAGRIELPSIPDDCKHNAHMFYIKLRDLEDR--SALINFLKE 311
Query: 121 Q 121
Sbjct: 312 A 312
>gnl|CDD|115557 pfam06907, Latexin, Latexin. This family consists of several
animal specific latexin proteins. Latexin is a
carboxypeptidase A inhibitor and is expressed in a cell
type-specific manner in both central and peripheral
nervous systems in the rat.
Length = 220
Score = 25.6 bits (56), Expect = 8.4
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 4/45 (8%)
Query: 120 NQKYGPRVSVESKHTIDLRPAIE---RLREHYKHLK-PIDSERIP 160
NQK P V+V + I + E R + K LK P++++ IP
Sbjct: 77 NQKPRPEVNVTCERLIGKKKRQEEDYRFYKQLKQLKRPLEAQSIP 121
>gnl|CDD|161784 TIGR00238, TIGR00238, KamA family protein. Note that the E. coli
homolog was expressed in E. coli and purified and found
not to display display lysine 2,3-aminomutase activity.
Active site residues are found in 100 residue extension
in B. subtilis. Name changed to KamA family protein.
Length = 331
Score = 25.6 bits (56), Expect = 8.7
Identities = 13/55 (23%), Positives = 21/55 (38%)
Query: 1 MSNLVKKAKKAVRAKKGCIYYSPELFAGILDQVANGKALGHVLRKVGMPKYSTFY 55
++ +A K +R + L G+ D+ L L KVG+ Y Y
Sbjct: 235 ITEEFAEAMKKLRTVNVTLLNQSVLLRGVNDRAQILAKLSIALFKVGIIPYYLHY 289
>gnl|CDD|162665 TIGR02025, BchH, magnesium chelatase, H subunit. This model
represents the H subunit of the magnesium chelatase
complex responsible for magnesium insertion into the
protoporphyrin IX ring in the biosynthesis of both
chlorophyll and bacteriochlorophyll. In
chlorophyll-utilizing species, this gene is known as
ChlH, while in bacteriochlorophyll-utilizing spoecies it
is called BchH. Subunit H is the largest (~140kDa) of
the three subunits (the others being BchD/ChlD and
BchI/ChlI), and is known to bind protoporphyrin IX.
Subunit H is homologous to the CobN subunit of
cobaltochelatase and by anology with that enzyme,
subunit H is believed to also bind the magnesium ion
which is inserted into the ring. In conjunction with the
hydrolysis of ATP by subunits I and D, a conformation
change is believed to happen in subunit H causing the
magnesium ion insertion into the distorted
protoporphyrin ring.
Length = 1216
Score = 25.5 bits (56), Expect = 9.4
Identities = 6/15 (40%), Positives = 11/15 (73%)
Query: 49 PKYSTFYRWIKKDLK 63
+++ FYRW+ +D K
Sbjct: 562 HQFAAFYRWLDRDFK 576
>gnl|CDD|161836 TIGR00358, 3_prime_RNase, VacB and RNase II family 3'-5'
exoribonucleases. This model is defined to identify a
pair of paralogous 3-prime exoribonucleases in E. coli,
plus the set of proteins apparently orthologous to one
or the other in other eubacteria. VacB was characterized
originally as required for the expression of virulence
genes, but is now recognized as the exoribonuclease
RNase R (Rnr). Its paralog in E. coli and H. influenzae
is designated exoribonuclease II (Rnb). Both are
involved in the degradation of mRNA, and consequently
have strong pleiotropic effects that may be difficult to
disentangle. Both these proteins share domain-level
similarity (RNB, S1) with a considerable number of other
proteins, and full-length similarity scoring below the
trusted cutoff to proteins associated with various
phenotypes but uncertain biochemistry; it may be that
these latter proteins are also 3-prime exoribonucleases.
Length = 654
Score = 25.4 bits (56), Expect = 9.5
Identities = 20/62 (32%), Positives = 27/62 (43%), Gaps = 5/62 (8%)
Query: 69 TEALQCRLDLLAEELLEEPAPTAEELANPVFYSKMRDRKQR-----MGTFLLEKLSNQKY 123
+ LQ L+ LAE L P AE + +R+ K R + T LL LS +Y
Sbjct: 425 KKKLQSLLEFLAELGLTLPGGNAENVTTLDGACWLREVKDRPEYEILVTRLLRSLSQAEY 484
Query: 124 GP 125
P
Sbjct: 485 SP 486
>gnl|CDD|162266 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH.
Length = 495
Score = 25.3 bits (56), Expect = 9.6
Identities = 15/37 (40%), Positives = 21/37 (56%), Gaps = 6/37 (16%)
Query: 64 LQEAYTEALQC------RLDLLAEELLEEPAPTAEEL 94
++EAY A Q L+LLA+ LLE+ T EE+
Sbjct: 454 IEEAYKRAKQILTENRDELELLAKALLEKETITREEI 490
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
0.316 0.133 0.375
Gapped
Lambda K H
0.267 0.0658 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,056,938
Number of extensions: 194148
Number of successful extensions: 462
Number of sequences better than 10.0: 1
Number of HSP's gapped: 462
Number of HSP's successfully gapped: 33
Length of query: 185
Length of database: 5,994,473
Length adjustment: 88
Effective length of query: 97
Effective length of database: 4,092,969
Effective search space: 397017993
Effective search space used: 397017993
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 54 (24.7 bits)