RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 020672
(323 letters)
>gnl|CDD|216656 pfam01709, Transcrip_reg, Transcriptional regulator. This is a
family of transcriptional regulators. In mammals, it
activates the transcription of mitochondrially-encoded
COX1. In bacteria, it negatively regulates the
quorum-sensing response regulator by binding to its
promoter region.
Length = 234
Score = 246 bits (631), Expect = 1e-81
Identities = 95/244 (38%), Positives = 139/244 (56%), Gaps = 14/244 (5%)
Query: 78 RRSSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKD 137
+ + I RK AQDAK+ K+++++GKE+ A K GGP+P N L +EKAK ++PKD
Sbjct: 1 SKWANIKHRKAAQDAKRGKIFTKLGKEITVAAKMGGPDPEGNPRLRLAIEKAKAANMPKD 60
Query: 138 IVERNIKRAS-EKGQEAFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKM 196
+ER IK+ S E + E YE YG GGV+I+VE LTD R+ A VR GG +
Sbjct: 61 NIERAIKKGSGGLDGENYEEIRYEGYGPGGVAIIVECLTDNRNRTAADVRHAFSKNGGNL 120
Query: 197 ADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYK 256
+ GSV + F R V+ + D+D+LL+ AL+AGAEDV E ED + +
Sbjct: 121 GETGSVSYMFDRKGVIVFEKEGVDEDELLEAALEAGAEDVEE----EDGS--------IE 168
Query: 257 VVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELDDVD 316
V++ ++ + L EAG+ E ++P T+E+D+E E ++LI L +LDDV
Sbjct: 169 VITDPTDFEAVKKALEEAGLEIE-SAEITMIPQNTVELDEEDAEKLEKLIDALEDLDDVQ 227
Query: 317 AVYT 320
VY
Sbjct: 228 NVYH 231
>gnl|CDD|223295 COG0217, COG0217, Uncharacterized conserved protein [Function
unknown].
Length = 241
Score = 206 bits (526), Expect = 1e-65
Identities = 95/241 (39%), Positives = 141/241 (58%), Gaps = 14/241 (5%)
Query: 81 SKIAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVE 140
+ I RK AQDAK++K+++++ KE+ A K+GGP+P SN L +EKAK ++PKD +E
Sbjct: 8 ANIKHRKAAQDAKRSKIFTKLIKEITVAAKQGGPDPESNPRLRTAIEKAKAANMPKDNIE 67
Query: 141 RNIKRAS-EKGQEAFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADP 199
R IK+AS K + E YE YG GGV+I+VE LTD R+ + VR GG + +P
Sbjct: 68 RAIKKASGGKDGANYEEIRYEGYGPGGVAIIVEALTDNRNRTASNVRSAFNKNGGNLGEP 127
Query: 200 GSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVS 259
GSV + F R V+ ++ + D+D+LL+ A++AGAEDV E DE E V +
Sbjct: 128 GSVSYMFDRKGVIVVEKNEIDEDELLEAAIEAGAEDVEE--------DEGSIE----VYT 175
Query: 260 TSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELDDVDAVY 319
+++ + L AG E+ ++P T+E+DDE E ++LI L + DDV VY
Sbjct: 176 EPEDFNKVKEALEAAGYEIESA-ELTMIPQNTVELDDEDAEKLEKLIDALEDDDDVQNVY 234
Query: 320 T 320
Sbjct: 235 H 235
>gnl|CDD|234640 PRK00110, PRK00110, hypothetical protein; Validated.
Length = 245
Score = 205 bits (524), Expect = 3e-65
Identities = 92/246 (37%), Positives = 140/246 (56%), Gaps = 23/246 (9%)
Query: 81 SK---IAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKD 137
SK I RKGAQDAK+ K+++++ +E+ A K GG +P N L ++KAK ++PKD
Sbjct: 5 SKWANIKHRKGAQDAKRGKIFTKLIREITVAAKLGGGDPEGNPRLRLAIDKAKAANMPKD 64
Query: 138 IVERNIKRAS-EKGQEAFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKM 196
+ER IK+ + E + E YE YG GGV+I+VE LTD R+ A VR GG +
Sbjct: 65 NIERAIKKGTGELDGANYEEIRYEGYGPGGVAIIVEALTDNRNRTAAEVRHAFSKNGGNL 124
Query: 197 ADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYK 256
+ GSV + F R V I D+D+L++ AL+AGAEDV TD++ ++
Sbjct: 125 GETGSVSYMFDRKGV--IVIEPLDEDELMEAALEAGAEDVE--------TDDE----SFE 170
Query: 257 VVSTSDNYTDITTKLREAGIPFETDNGSEL--LPITTIEVDDEAMELNKELIAKLLELDD 314
V++ +++ + L AG+ E+ +E+ +P T+E+D+E E +LI L +LDD
Sbjct: 171 VITAPEDFEAVRDALEAAGLEAES---AEVTMIPQNTVELDEETAEKLLKLIDALEDLDD 227
Query: 315 VDAVYT 320
V VY
Sbjct: 228 VQNVYH 233
>gnl|CDD|237084 PRK12378, PRK12378, hypothetical protein; Provisional.
Length = 235
Score = 195 bits (497), Expect = 3e-61
Identities = 87/245 (35%), Positives = 128/245 (52%), Gaps = 13/245 (5%)
Query: 76 MGRRSSKIAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVP 135
MGR I +K +D K+K+++++GKE+ A K+GGP+P SN L V+E+AK+ +VP
Sbjct: 1 MGRAWENIKAKKAKKDGAKSKIFAKLGKEIYVAAKQGGPDPESNPALRFVIERAKKANVP 60
Query: 136 KDIVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGK 195
KD++ER IK+A G E + E YE +G GV ++VE LTD + R+VA VR GG
Sbjct: 61 KDVIERAIKKAKGGGGEDYEEVRYEGFGPNGVMVIVECLTDNVNRTVANVRSAFNKNGGN 120
Query: 196 MADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYY 255
+ GSV F F V + D D+ I D EDV E E+ T
Sbjct: 121 LGTSGSVAFMFDHKGVFVFEGDDEDELLEALIDADVDVEDVEE----EEGT--------I 168
Query: 256 KVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLELDDV 315
V + ++ + L AGI F E++P +E+ E +E ++L+ L + DDV
Sbjct: 169 TVYTDPTDFHKVKKALEAAGIEFLVAE-LEMIPQNPVELSGEDLEQFEKLLDALEDDDDV 227
Query: 316 DAVYT 320
VY
Sbjct: 228 QNVYH 232
>gnl|CDD|233240 TIGR01033, TIGR01033, DNA-binding regulatory protein, YebC/PmpR
family. This model describes a minimally characterized
protein family, restricted to bacteria excepting for
some eukaryotic sequences that have possible transit
peptides. YebC from E. coli is crystallized, and PA0964
from Pseudomonas aeruginosa has been shown to be a
sequence-specific DNA-binding regulatory protein
[Regulatory functions, DNA interactions].
Length = 238
Score = 189 bits (483), Expect = 3e-59
Identities = 91/248 (36%), Positives = 134/248 (54%), Gaps = 16/248 (6%)
Query: 76 MGRRSSK--IAGRKGAQDAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELD 133
M S I RK AQDAK+ K+++++ KE+I A K GG +P SN L +EKAK +
Sbjct: 1 MAGHSKWANIKHRKAAQDAKRGKIFTKLIKEIIVAAKLGGGDPESNPRLRTAIEKAKAAN 60
Query: 134 VPKDIVERNIKRA-SEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDC 192
+PKD +ER IK+ E + E YE Y GGV+I+VE LTD R+ + VR
Sbjct: 61 MPKDNIERAIKKGAGELDGSNYEEITYEGYAPGGVAIIVECLTDNKNRTASEVRSAFNKN 120
Query: 193 GGKMADPGSVMFKFRRARVVNIKFTDADKDQLLDIALDAGAEDVIEPPVNEDDTDEDRAE 252
GG + +PGSV + F R V+ + + D++ L++ A++AGAED+ D D+D E
Sbjct: 121 GGSLGEPGSVSYLFSRKGVIEVPKNEVDEEDLMEAAIEAGAEDI--------DVDDDEFE 172
Query: 253 RYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAKLLEL 312
V + + + L G P E ++P+TT+++DDE E +LI L +
Sbjct: 173 ----VYTAPEELEKVKEALEAKGFPIE-SAEITMIPLTTVDLDDEQAEKLLKLIDALEDD 227
Query: 313 DDVDAVYT 320
DDV VY
Sbjct: 228 DDVQEVYH 235
>gnl|CDD|143552 cd07443, CRD_SFRP1, Cysteine-rich domain of the secreted
frizzled-related protein 1 (SFRP1), a regulator of Wnt
activity. The cysteine-rich domain (CRD) is an
essential part of the secreted frizzled-related protein
1 (SFRP1), which regulates the activity of Wnt
proteins, key players in a number of fundamental
cellular processes such as embryogenesis and postnatal
development. SFRPs antagonize the activation of Wnt
signaling by binding to the CRDs domains of frizzled
(Fz) proteins, thereby preventing Wnt proteins from
binding to these receptors. SFRPs are also known to
have functions unrelated to Wnt, as enhancers of
procollagen cleavage by the TLD proteinases. SFRPs and
Fz proteins both contain CRD domains, but SFRPs lack
the seven-pass transmembrane domain which is an
integral part of Fzs. SFRP1 is expressed in many
tissues and is involved in the regulation of Wnt
signaling in osteoblasts, leading to enhanced
trabecular bone formation in adults; it has also been
shown to control the growth of retinal ganglion cell
axons and the elongation of the antero-posterior axis.
Length = 124
Score = 32.6 bits (74), Expect = 0.092
Identities = 14/30 (46%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 50 SSWIPLYEVK-HCNFQVRTIRTFAPVCMGR 78
SSW+PL H QV FAPVC+ R
Sbjct: 44 SSWVPLLNKNCHKGTQVFLCSLFAPVCLDR 73
>gnl|CDD|143553 cd07444, CRD_SFRP5, Cysteine-rich domain of the secreted
frizzled-related protein 5 (SFRP5), a regulator of Wnt
activity. The cysteine-rich domain (CRD) is an
essential part of the secreted frizzled-related Protein
5 (SFRP5), which regulates the activity of Wnt
proteins, key players in a number of fundamental
cellular processes such as embryogenesis and postnatal
development. SFRPs antagonize the activation of Wnt
signaling by binding to the CRD domains of frizzled
(Fz) proteins, thereby preventing Wnt proteins from
binding to these receptors. SFRPs are also known to
have functions unrelated to Wnt, as enhancers of
procollagen cleavage by the TLD proteinases. SFRPs and
Fz proteins both contain CRD domains, but SFRPs lack
the seven-pass transmembrane domain which is an
integral part of Fzs.
Length = 127
Score = 31.8 bits (72), Expect = 0.18
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 50 SSWIPLYEVK-HCNFQVRTIRTFAPVCMGR 78
SSW+PL + H + QV FAPVC+ R
Sbjct: 44 SSWVPLLAKRCHADTQVFLCSLFAPVCLDR 73
>gnl|CDD|221101 pfam11382, DUF3186, Protein of unknown function (DUF3186). This
bacterial family of proteins has no known function.
Length = 307
Score = 31.2 bits (71), Expect = 0.60
Identities = 35/220 (15%), Positives = 69/220 (31%), Gaps = 31/220 (14%)
Query: 113 GPNPTSNTVLAAVLEKAKELDVPKDIV--ERNIKRASEKGQEAFIEKVYEVY---GYGGV 167
G +L+ + ++ +L D + ER + FI + G
Sbjct: 25 GSGLLQENLLSGLEDEFSDLRTENDRLRAEREALNEQASAADQFIAALAPRLVAGRLTGK 84
Query: 168 SIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMFKFRRARVVNIKFTDADK-DQLLD 226
S+ + D V AV E + G + G + + F D + D+L
Sbjct: 85 SVALVRTPDADDDDVDAVSEALTQAGATVV--GRI--------TLTDNFVDPESADKLKS 134
Query: 227 IALDAGAEDVIEPPVNEDDTDEDRAERYYKVV------STSDNYTDITTKLREAGIPFET 280
+ + + D + + ++++ + + LR+AG T
Sbjct: 135 VVNNDLKPAGDQLSTAAADPGSQAGDLLGAALLLNPPTASTEERSAVLAALRDAG--LIT 192
Query: 281 DNGSELLPITTIEV-------DDEAMELNKELIAKLLELD 313
+G + P V D +A L+ + LD
Sbjct: 193 YSGDTVGPADAAVVVGGDSAGDADANALDAAVARFARALD 232
>gnl|CDD|223946 COG1014, PorG, Pyruvate:ferredoxin oxidoreductase and related
2-oxoacid:ferredoxin oxidoreductases, gamma subunit
[Energy production and conversion].
Length = 203
Score = 30.4 bits (69), Expect = 0.81
Identities = 16/63 (25%), Positives = 24/63 (38%), Gaps = 14/63 (22%)
Query: 108 AVKKGGPNPTSNTVLAAVL-------------EKAKELDVPKDIVERNIKRASEKGQEAF 154
A ++ G +NTV+ E+A + +VE N+K A E G E
Sbjct: 134 AAEEAGGRIIANTVMLGAFAALTGIVPELEALEEAIKARFKGKVVEANLK-AFEAGYEEA 192
Query: 155 IEK 157
E
Sbjct: 193 EEV 195
>gnl|CDD|216304 pfam01113, DapB_N, Dihydrodipicolinate reductase, N-terminus.
Dihydrodipicolinate reductase (DapB) reduces the
alpha,beta-unsaturated cyclic imine,
dihydro-dipicolinate. This reaction is the second
committed step in the biosynthesis of L-lysine and its
precursor meso-diaminopimelate, which are critical for
both protein and cell wall biosynthesis. The N-terminal
domain of DapB binds the dinucleotide NADPH.
Length = 122
Score = 28.8 bits (65), Expect = 1.5
Identities = 10/41 (24%), Positives = 19/41 (46%), Gaps = 5/41 (12%)
Query: 100 RMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVE 140
RMG+E+I A+ + + L A +++ + D E
Sbjct: 11 RMGRELIKAILE-----APDFELVAAVDRPGSSLLGSDAGE 46
>gnl|CDD|226857 COG4449, COG4449, Predicted protease of the Abi (CAAX) family
[General function prediction only].
Length = 827
Score = 29.6 bits (66), Expect = 2.7
Identities = 17/69 (24%), Positives = 30/69 (43%), Gaps = 11/69 (15%)
Query: 247 DEDRAERYYKVVSTSDNYTDITTKLREAGI--PFETDNGSELLPITTIE----VDD---- 296
+RY K+V+T N+T K +AG P + S++ P+ ++ VDD
Sbjct: 112 SNADLDRYLKLVTTDVNFTPAALKSEQAGNLLPNRLNGRSQVGPLQSLAGARPVDDVLVR 171
Query: 297 -EAMELNKE 304
++N
Sbjct: 172 FVQAQVNVP 180
>gnl|CDD|235668 PRK06007, fliF, flagellar MS-ring protein; Reviewed.
Length = 542
Score = 29.1 bits (66), Expect = 3.7
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 7/55 (12%)
Query: 255 YKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIEVD-DEAMELNKELIAK 308
Y +S D I L +AGIP++ + TI V D+ EL +L ++
Sbjct: 54 YSNLSDQD-AGQIVAALDQAGIPYKVADDG-----GTILVPADKVDELRLKLASE 102
>gnl|CDD|107298 cd06303, PBP1_LuxPQ_Quorum_Sensing, Periplasmic binding protein
(LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from
Vibrio harveyi and its close homologs. Periplasmic
binding protein (LuxP) of autoinducer-2 (AI-2) receptor
LuxPQ from Vibrio harveyi and its close homologs from
other bacteria. The members of this group are highly
homologous to a family of periplasmic pentose/hexose
sugar-binding proteins that function as the primary
receptors for chemotaxis and transport of many sugar
based solutes in bacteria and archaea, and that are
members of the type I periplasmic binding protein
superfamily. The Vibrio harveyi AI-2 receptor consists
of two polypeptides, LuxP and LuxQ: LuxP is a
periplasmic binding protein that binds AI-2 by clamping
it between two domains, LuxQ is an integral membrane
protein belonging to the two-component sensor kinase
family. Unlike AI-2 bound to the LsrB receptor in
Salmonella typhimurium, the Vibrio harveyi AI-2
signaling molecule has an unusual furanosyl borate
diester. Hence, many bacteria coordinate their gene
expression according to the local density of their
population by producing species specific AI-2. This
process of quorum sensing allows LuxPQ to control light
production as well as its motility behavior.
Length = 280
Score = 28.9 bits (65), Expect = 3.8
Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 7/58 (12%)
Query: 255 YKVVSTSD----NYTDITTKLREAGIPFETDNGSELLPITTIEVDDEAMELNKELIAK 308
Y SD N T +L E IP+E + I+ ++ +LN+ L +K
Sbjct: 6 YPGQQISDYWVRNIASFTARLEELNIPYELT---QFSSRPGIDHRLQSQQLNEALQSK 60
>gnl|CDD|226048 COG3517, COG3517, Predicted component of the type VI protein
secretion system [Intracellular trafficking, secretion,
and vesicular transport].
Length = 495
Score = 28.9 bits (65), Expect = 3.9
Identities = 14/38 (36%), Positives = 22/38 (57%), Gaps = 1/38 (2%)
Query: 128 KAKELDVPKDIVERNIKRASEKGQEAFIEKVYEVYGYG 165
K + L++ KD + R+ ++A E Q +KVYE YG
Sbjct: 116 KIRVLNISKDELLRDFEKAPEFDQSGLFKKVYE-EEYG 152
>gnl|CDD|219605 pfam07847, DUF1637, Protein of unknown function (DUF1637). This
family contains many eukaryotic hypothetical proteins.
The region featured in this family is approximately 120
residues long. According to InterPro annotation, some
members of this family may belong to the cupin
superfamily.
Length = 194
Score = 28.4 bits (64), Expect = 4.0
Identities = 12/43 (27%), Positives = 15/43 (34%), Gaps = 3/43 (6%)
Query: 235 DVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIP 277
DV+ PP + DD R YY+ L E P
Sbjct: 140 DVLAPPYDPDD---GRDCTYYRDSPLPSGLPSEAAWLEEIPQP 179
>gnl|CDD|176237 cd08276, MDR7, Medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family.
This group is a member of the medium chain
dehydrogenases/reductase (MDR)/zinc-dependent alcohol
dehydrogenase-like family, but lacks the zinc-binding
sites of the zinc-dependent alcohol dehydrogenases. The
medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P)-binding Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 336
Score = 28.7 bits (65), Expect = 4.1
Identities = 24/87 (27%), Positives = 36/87 (41%), Gaps = 20/87 (22%)
Query: 101 MGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVYE 160
G VI+ TS++ LE+AK L I N + + G+E +
Sbjct: 183 AGARVIA---------TSSS--DEKLERAKALGADHVI---NYRTTPDWGEEVL-----K 223
Query: 161 VYGYGGVSIVVEVL-TDKITRSVAAVR 186
+ G GV VVEV + +S+ AV
Sbjct: 224 LTGGRGVDHVVEVGGPGTLAQSIKAVA 250
>gnl|CDD|239094 cd02411, archeal_30S_S3_KH, K homology RNA-binding domain (KH) of
the archaeal 30S small ribosomal subunit S3 protein. S3
is part of the head region of the 30S ribosomal subunit
and is believed to interact with mRNA as it threads its
way from the latch into the channel. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In general, KH
binds single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA.
Length = 85
Score = 26.8 bits (60), Expect = 4.4
Identities = 15/46 (32%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 134 VPKDIVERNIKRASEKGQEAFIEKVYEVYGYGGVSIVVEVLTDKIT 179
V + V +KR ++EK E GYGG+ I+ L +IT
Sbjct: 1 VERKFVNEGVKRTMID---EYLEKELERAGYGGMEILRTPLGTQIT 43
>gnl|CDD|236490 PRK09376, rho, transcription termination factor Rho; Provisional.
Length = 416
Score = 28.6 bits (65), Expect = 5.4
Identities = 16/53 (30%), Positives = 29/53 (54%), Gaps = 9/53 (16%)
Query: 122 LAAVLEKAKELDVP-------KDIVERNIKRASEKGQEAFIEKVYEVY--GYG 165
L+ +LE A+EL + ++++ +K +EKG + F E V E+ G+G
Sbjct: 11 LSELLELAEELGIENASRLRKQELIFAILKAQAEKGGDIFGEGVLEILPDGFG 63
>gnl|CDD|235970 PRK07217, PRK07217, replication factor A; Reviewed.
Length = 311
Score = 28.4 bits (64), Expect = 5.6
Identities = 27/98 (27%), Positives = 42/98 (42%), Gaps = 21/98 (21%)
Query: 221 KDQLLDIALDAGAEDVIE---PPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIP 277
+Q D+ +D EDV E V E ED A R + L+EAGI
Sbjct: 12 HEQFSDLGVDVSVEDVEERLDTLVTEFKVPEDEARR-----------SVTNYYLKEAGID 60
Query: 278 ---FETDNGSELLPITTIEVDDEAMELNKELIAKLLEL 312
GSEL+ I I+ ++ +++ AK+++L
Sbjct: 61 RDELSGGGGSELVNIADIDEPEQWVDVT----AKVVQL 94
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 28.6 bits (63), Expect = 6.1
Identities = 14/59 (23%), Positives = 26/59 (44%)
Query: 240 PVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIPFETDNGSELLPITTIEVDDEA 298
+ E+ + ED VSTSD D+ ++ I E ++ +E + + DE+
Sbjct: 417 AIAEETSREDELSFDDSDVSTSDENEDVDFTGKKGAINNEDESDNEEVAFDSDSQFDES 475
>gnl|CDD|148673 pfam07209, DUF1415, Protein of unknown function (DUF1415). This
family consists of several hypothetical bacterial
proteins of around 180 residues in length. The function
of this family is unknown.
Length = 174
Score = 27.5 bits (62), Expect = 6.8
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 135 PKDIVERNIKRASEKGQEAFIE 156
P+ I ERNI G+E +
Sbjct: 152 PESIPERNIATLRRLGREGWKA 173
>gnl|CDD|153004 pfam12570, DUF3750, Protein of unknown function (DUF3750). This
family of proteins is found in bacteria. Proteins in
this family are typically between 175 and 265 amino
acids in length.
Length = 129
Score = 26.8 bits (60), Expect = 7.5
Identities = 11/21 (52%), Positives = 14/21 (66%)
Query: 114 PNPTSNTVLAAVLEKAKELDV 134
P P SNT +A VL + ELD+
Sbjct: 98 PGPNSNTFVAWVLRQVPELDL 118
>gnl|CDD|200253 TIGR03225, benzo_boxB, benzoyl-CoA oxygenase, B subunit. Members
of this protein family are BoxB, the B subunit of
benzoyl-CoA oxygenase. This oxygen-requiring enzyme acts
in an aerobic pathway of benzoate catabolism via
coenzyme A ligation [Energy metabolism, Other].
Length = 471
Score = 27.9 bits (62), Expect = 7.6
Identities = 17/66 (25%), Positives = 32/66 (48%)
Query: 100 RMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEKGQEAFIEKVY 159
R GK ++++ + G +P S T + E+A + V + V R I+R + +E + Y
Sbjct: 211 RDGKMQLASLAESGFDPLSRTCRFMLTEEAHHMFVGESGVGRVIQRTCQVMKELGTDDPY 270
Query: 160 EVYGYG 165
+ G
Sbjct: 271 RIRALG 276
>gnl|CDD|227277 COG4941, COG4941, Predicted RNA polymerase sigma factor containing
a TPR repeat domain [Transcription].
Length = 415
Score = 27.8 bits (62), Expect = 8.3
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 269 TKLREAGIPFETDNGSEL 286
++REAGIPFE EL
Sbjct: 162 ARIREAGIPFEVPGPQEL 179
>gnl|CDD|223923 COG0854, PdxJ, Pyridoxal phosphate biosynthesis protein [Coenzyme
metabolism].
Length = 243
Score = 27.6 bits (62), Expect = 8.3
Identities = 24/94 (25%), Positives = 35/94 (37%), Gaps = 19/94 (20%)
Query: 222 DQLLDIALDAGAEDVIEPPVNEDDTDEDRAERYYKVVSTSDNYTDITTKLREAGIP---F 278
+++L IAL V P + +E E V D D +L+ AGI F
Sbjct: 74 EEMLAIALKTKPHQVTLVP---EKREEVTTEGGLDVAGQLDKLRDAVRRLKNAGIRVSLF 130
Query: 279 ETDNGSELLPITTIEVDDEAMELNKELIAKLLEL 312
I+ D E +E E+ A +EL
Sbjct: 131 -------------IDPDPEQIEAAAEVGAPRIEL 151
>gnl|CDD|240349 PTZ00295, PTZ00295, glucosamine-fructose-6-phosphate
aminotransferase; Provisional.
Length = 640
Score = 28.1 bits (63), Expect = 8.5
Identities = 9/27 (33%), Positives = 17/27 (62%)
Query: 260 TSDNYTDITTKLREAGIPFETDNGSEL 286
T +NY ++ ++L GI F ++ SE+
Sbjct: 132 TIENYVELKSELIAKGIKFRSETDSEV 158
>gnl|CDD|238315 cd00562, NifX_NifB, This CD represents a family of iron-molybdenum
cluster-binding proteins that includes NifB, NifX, and
NifY, all of which are involved in the synthesis of an
iron-molybdenum cofactor (FeMo-co) that binds the active
site of the dinitrogenase enzyme. This domain is a
predicted small-molecule-binding domain (SMBD) with an
alpha/beta fold that is present either as a stand-alone
domain (e.g. NifX and NifY) or fused to another
conserved domain (e.g. NifB) however, its function is
still undetermined.The SCOP database suggests that this
domain is most similar to structures within the
ribonuclease H superfamily. This conserved domain is
represented in two of the three major divisions of life
(bacteria and archaea).
Length = 102
Score = 26.4 bits (59), Expect = 8.6
Identities = 13/47 (27%), Positives = 19/47 (40%), Gaps = 2/47 (4%)
Query: 278 FETDNGSELLPITTIEVDDEAMELNKE-LIAKLLELDDVDAVYTDQI 323
+E + G L + E + L A+LL L+ DAV I
Sbjct: 25 YEVEPGGIKL-VEVRENPAACGGGGEGKLAARLLALEGCDAVLVGGI 70
>gnl|CDD|215487 PLN02900, PLN02900, alanyl-tRNA synthetase.
Length = 936
Score = 28.1 bits (63), Expect = 9.0
Identities = 28/114 (24%), Positives = 46/114 (40%), Gaps = 13/114 (11%)
Query: 91 DAKKAKLYSRMGKEVISAVKKGGPNPTSNTVLAAVLEKAKELDVPKDIVERNIKRASEKG 150
+ K A L SR+ VI A KK ++A+ ++ + K+ K A K
Sbjct: 765 EKKVASLKSRVDAAVIPAAKKE----EIRARVSALQKELRAAQ--KEAAALRAKLAVAKA 818
Query: 151 QEAFIEKVYEVYGYGGVSIVVEVLTDKITRSVAAVREVVKDCGGKMADPGSVMF 204
E K G S++V L + AA++E + K+ DP +V+
Sbjct: 819 TEL-ASKALSA----GKSVLVARLDVGV--DAAALKEAAEKVIAKLGDPAAVVL 865
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
0.314 0.131 0.364
Gapped
Lambda K H
0.267 0.0609 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 16,442,702
Number of extensions: 1625984
Number of successful extensions: 1788
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1773
Number of HSP's successfully gapped: 59
Length of query: 323
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 226
Effective length of database: 6,635,264
Effective search space: 1499569664
Effective search space used: 1499569664
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: 42 (22.0 bits)
S2: 59 (26.8 bits)