RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12259
(848 letters)
>gnl|CDD|226508 COG4021, COG4021, Uncharacterized conserved protein [Function
unknown].
Length = 249
Score = 251 bits (643), Expect = 9e-78
Identities = 94/207 (45%), Positives = 127/207 (61%), Gaps = 5/207 (2%)
Query: 598 CFMEFESHDRCLPNCFIVVRVDGKGFHKFTEAHGFDKPNDRSGLWLMSKAAACVIEEF-N 656
E +HDR LP +IV+R+DG+GFHKFT+ F+KP D L LM+ A ++ ++
Sbjct: 7 YVREVYAHDRILPQTYIVLRIDGRGFHKFTKFLDFEKPYDERFLKLMNATAKNLVLKYGL 66
Query: 657 DICCAYGQSDEYSFIFSRNTNIYNRRADKIASVVCSLFTSSYGFYWDKFCCKKLKYPPAF 716
DI AY SDE SF+ +T +N R +K+ SV S FTS++ W KF K+ P+F
Sbjct: 67 DIILAYTFSDEISFLLKSSTVPFNGRVEKLDSVFASFFTSAFTRLWAKF--FPEKHLPSF 124
Query: 717 DSRVILYPTVRNLRDYLSWRQADAHINNLYNTAFWGLVQKCGHSKQEAEKILRGTVSSEK 776
DSR + YP + DY WRQ +A NNLY+T FW L+ G + QEAE+ LRGT S+EK
Sbjct: 125 DSRCVAYPL-DTIPDYFHWRQVEAWRNNLYSTTFWQLII-RGLTPQEAEERLRGTKSNEK 182
Query: 777 HELLFKDCKINYNNECELYKKGTIIIK 803
HE+LF + INYN E E KKG + +
Sbjct: 183 HEILFSEFGINYNREPEWQKKGVGVYR 209
Score = 128 bits (324), Expect = 2e-33
Identities = 49/119 (41%), Positives = 67/119 (56%), Gaps = 4/119 (3%)
Query: 447 FLHKKFNDICCAYGQSDEYSFIFSRNTNIYNRRADKIASVVCSLFTSSYGFYWDKFCCKK 506
+ K DI AY SDE SF+ +T +N R +K+ SV S FTS++ W KF
Sbjct: 60 LVLKYGLDIILAYTFSDEISFLLKSSTVPFNGRVEKLDSVFASFFTSAFTRLWAKF--FP 117
Query: 507 LKYPPAFDSRVILYPTVRNLRDYLSWRQADAHINNLYNTAFWGLVQKCGHSKQEPLKQL 565
K+ P+FDSR + YP + DY WRQ +A NNLY+T FW L+ G + QE ++L
Sbjct: 118 EKHLPSFDSRCVAYPL-DTIPDYFHWRQVEAWRNNLYSTTFWQLII-RGLTPQEAEERL 174
>gnl|CDD|203016 pfam04446, Thg1, tRNAHis guanylyltransferase. The Thg1 protein
from Saccharomyces cerevisiae is responsible for adding
a GMP residue to the 5' end of tRNA His. The catalytic
domain Thg1 contains a RRM (ferredoxin) fold palm
domain, just like the viral RNA-dependent RNA
polymerases, reverse transcriptases, family A and B DNA
polymerases, adenylyl cyclases, diguanylate cyclases
(GGDEF domain) and the predicted polymerase of the
CRISPR system. Thg1 possesses an active site with three
acidic residues that chelate Mg++ cations. Thg1
catalyzes polymerization similar to the 5'-3'
polymerases.
Length = 131
Score = 199 bits (508), Expect = 6e-60
Identities = 75/125 (60%), Positives = 95/125 (76%), Gaps = 1/125 (0%)
Query: 601 EFESHDRCLPNCFIVVRVDGKGFHKFTEAHGFDKPNDRSGLWLMSKAAACVIEEFNDICC 660
+FE DR LPN IVVR+DG+GFHKFT+ HGF+KPND L LM+ AA ++EEF DI
Sbjct: 7 QFEQDDRLLPNTPIVVRIDGRGFHKFTKKHGFEKPNDERALDLMNAAAKALMEEFPDIVL 66
Query: 661 AYGQSDEYSFIFSRNTNIYNRRADKIASVVCSLFTSSYGFYWDK-FCCKKLKYPPAFDSR 719
AYGQSDE SF+F ++T ++NRR +K+ SVV SLF+SS+ + W K F K LKYPP+FD R
Sbjct: 67 AYGQSDEISFLFRKDTLLFNRRVEKLVSVVASLFSSSFVYKWGKFFPDKPLKYPPSFDGR 126
Query: 720 VILYP 724
V+LYP
Sbjct: 127 VVLYP 131
Score = 114 bits (288), Expect = 8e-30
Identities = 42/73 (57%), Positives = 56/73 (76%), Gaps = 1/73 (1%)
Query: 450 KKFNDICCAYGQSDEYSFIFSRNTNIYNRRADKIASVVCSLFTSSYGFYWDK-FCCKKLK 508
++F DI AYGQSDE SF+F ++T ++NRR +K+ SVV SLF+SS+ + W K F K LK
Sbjct: 59 EEFPDIVLAYGQSDEISFLFRKDTLLFNRRVEKLVSVVASLFSSSFVYKWGKFFPDKPLK 118
Query: 509 YPPAFDSRVILYP 521
YPP+FD RV+LYP
Sbjct: 119 YPPSFDGRVVLYP 131
>gnl|CDD|222741 pfam14413, Thg1C, Thg1 C terminal domain. Thg1 polymerases contain
an additional region of conservation C-terminal to the
core palm domain that comprise of 5 helices and two
strands. This region has several well-conserved charged
residues including a basic residue found towards the end
of the first helix of this unit might contribute to the
Thg1-specific active site. This C-terminal module of
Thg1 is predicted to form a helical bundle that
functions equivalently to the fingers of the other
nucleic acid polymerases, probably in interacting with
the template HtRNA.
Length = 120
Score = 147 bits (372), Expect = 2e-41
Identities = 56/122 (45%), Positives = 78/122 (63%), Gaps = 11/122 (9%)
Query: 725 TVRNLRDYLSWRQADAHINNLYNTAFWGLVQKCGHSKQEAEKILRGTVSSEKHELLFKDC 784
++ +RDYLSWRQADAH NNLYNTAFW LV K G S +EA + L+GT+SS+K+ELLF +
Sbjct: 1 SLEEVRDYLSWRQADAHRNNLYNTAFWALV-KGGFSPKEATERLKGTLSSDKNELLFSEF 59
Query: 785 KINYNNECELYKKGTIIIKSLVPSSTGSPVCNTVY---------VPLNCDIINDKFWNEN 835
INYNNE +++G+++ + V +P +PL CDI ++ FW E
Sbjct: 60 GINYNNEPAWFRRGSLLYREEVEKEGYNPKTGEKVKVKRRRDSELPLFCDIGDE-FWEEL 118
Query: 836 PH 837
P+
Sbjct: 119 PY 120
Score = 72.7 bits (179), Expect = 2e-15
Identities = 27/39 (69%), Positives = 31/39 (79%), Gaps = 1/39 (2%)
Query: 522 TVRNLRDYLSWRQADAHINNLYNTAFWGLVQKCGHSKQE 560
++ +RDYLSWRQADAH NNLYNTAFW LV K G S +E
Sbjct: 1 SLEEVRDYLSWRQADAHRNNLYNTAFWALV-KGGFSPKE 38
>gnl|CDD|222190 pfam13517, VCBS, Family description. This domain of about 100
residues is found in multiple (up to 35) copies in long
proteins from several species of Vibrio, Colwellia,
Bradyrhizobium, and Shewanella (hence the name VCBS) and
in smaller copy numbers in proteins from several other
bacteria. The large protein size and repeat copy
numbers, species distribution, and suggested activities
of several member proteins suggests a role for this
domain in adhesion (TIGR).
Length = 61
Score = 39.5 bits (93), Expect = 3e-04
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 1/62 (1%)
Query: 88 DINLDGVLDCIVIADNGYLAVLSQATGNLLWRKTNNGYKDGKMKFPLIVDDLTGDGVNDL 147
D++ DG LD +V+A +G + + T+ G + V DL GDG DL
Sbjct: 1 DLDGDGRLD-LVVASDGGVRLYLNNGDGTFTFVTSTLLGTGGGGTSVAVADLDGDGDLDL 59
Query: 148 VL 149
++
Sbjct: 60 LV 61
>gnl|CDD|234163 TIGR03300, assembly_YfgL, outer membrane assembly lipoprotein YfgL.
Members of this protein family are YfgL, a lipoprotein
component of a complex that acts protein insertion into
the bacterial outer membrane. Other members of this
complex are NlpB, YfiO, and YaeT. This protein contains
multiple copies of a repeat that, in other contexts, are
associated with binding of the coenzyme PQQ [Protein
fate, Protein and peptide secretion and trafficking].
Length = 377
Score = 36.4 bits (85), Expect = 0.060
Identities = 26/101 (25%), Positives = 48/101 (47%), Gaps = 20/101 (19%)
Query: 44 QMSLRSGQPPPT-----------GGGLIALDSVRPVELWRKTLNNVPK---EVDCGLIDI 89
++LR G P GG L+AL+ LW + + +PK E++ L+D+
Sbjct: 177 ALTLR-GSASPVIADGGVLVGFAGGKLVALNLQTGQPLWEQRVA-LPKGRTELE-RLVDV 233
Query: 90 NLDGVLD---CIVIADNGYLAVLSQATGNLLWRKTNNGYKD 127
+ D V+D ++ G +A L +G +LW++ + Y+
Sbjct: 234 DGDPVVDGGQVYAVSYQGRVAALDLRSGRVLWKRDASSYQG 274
Score = 30.3 bits (69), Expect = 4.7
Identities = 19/69 (27%), Positives = 28/69 (40%), Gaps = 7/69 (10%)
Query: 56 GGGLIALDSVRPVELWRKTLNNVPKEVDCGLIDINLDGVLDCIVIADNGYLAVLSQATGN 115
G ++ALD+ LWR L+ + G + DG L V + G + L G
Sbjct: 74 DGTVVALDAETGKRLWRVDLDE---RLSGG---VGADGGL-VFVGTEKGEVIALDAEDGK 126
Query: 116 LLWRKTNNG 124
LWR +
Sbjct: 127 ELWRAKLSS 135
>gnl|CDD|222072 pfam13360, PQQ_2, PQQ-like domain. This domain contains several
repeats of the PQQ repeat.
Length = 234
Score = 34.3 bits (79), Expect = 0.20
Identities = 21/65 (32%), Positives = 28/65 (43%), Gaps = 7/65 (10%)
Query: 55 TGGGLIALDSVRPVELWRKTLNNVPKEVDCGLIDINLDGVLDCIVIADNGYLAVLSQATG 114
G L+ALD+ LWRK L+ GV+ +V+ +G L L TG
Sbjct: 42 GKGELVALDAATGKLLWRKDLSGEILGAP-----TVAGGVV--VVVTADGSLYALDAETG 94
Query: 115 NLLWR 119
LLW
Sbjct: 95 KLLWS 99
>gnl|CDD|199834 cd10276, BamB_YfgL, Beta-barrel assembly machinery (Bam) complex
component B and related proteins. BamB (YflG) is a
non-essential component of the beta-barrel assembly
machinery (Bam), a multi-subunit complex that inserts
proteins with beta-barrel topology into the outer
membrane. BamB has been found to interact with BamA,
which in turn binds and stabilizes pre-folded
beta-barrel proteins; it has been suggested that BamB
participates in the stabilization.
Length = 358
Score = 32.7 bits (75), Expect = 0.72
Identities = 10/41 (24%), Positives = 17/41 (41%), Gaps = 3/41 (7%)
Query: 83 DCGLIDINLDGVLD---CIVIADNGYLAVLSQATGNLLWRK 120
+ID ++ V+ + GYL L +G LW +
Sbjct: 203 LPRMIDSSVTYVVVGGYLYSTSYQGYLVALDFESGQFLWSR 243
>gnl|CDD|224682 COG1768, COG1768, Predicted phosphohydrolase [General function
prediction only].
Length = 230
Score = 30.9 bits (70), Expect = 2.1
Identities = 20/97 (20%), Positives = 35/97 (36%), Gaps = 22/97 (22%)
Query: 290 NHTVYSFNASKTYIMQPLIIHFNNAA-----------NGFLLKYWEWQPDKEEQEDYYDK 338
NH + + SK P I+ + N G+ ++ +P E+ E + +
Sbjct: 82 NHDYWWSSISKLNNALPPILFYLNNGFELLNYAIVGVRGWDSPSFDSEPLTEQDEKIFLR 141
Query: 339 DKIIIIRHLQERI------VLVMF-----SPDGTPGP 364
+ + + +VM S DGTPGP
Sbjct: 142 EIGRLRLSADAALPKGVSKFIVMTHYPPFSDDGTPGP 178
>gnl|CDD|224600 COG1686, DacC, D-alanyl-D-alanine carboxypeptidase [Cell envelope
biogenesis, outer membrane].
Length = 389
Score = 31.2 bits (71), Expect = 2.3
Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 9/67 (13%)
Query: 625 KFTEAHGFDKPNDRSGLWLMSKAAACVIEEFNDICCAYGQSDEYSFIF------SRNTNI 678
F G D P + ++ A +I ++ +I Y S SF F RN N+
Sbjct: 162 HFVNPSGLDNPGQVTTARDLALLARALIRDYPEI---YEISSTKSFTFPANKITQRNRNL 218
Query: 679 YNRRADK 685
R
Sbjct: 219 LLWRKYP 225
>gnl|CDD|227326 COG4993, Gcd, Glucose dehydrogenase [Carbohydrate transport and
metabolism].
Length = 773
Score = 30.5 bits (69), Expect = 4.0
Identities = 21/103 (20%), Positives = 30/103 (29%), Gaps = 16/103 (15%)
Query: 104 GYLAVLSQATGNLLWRKTNNGYKDG-------KMKFPLIVDDLTGDGVNDLVLISYMGPS 156
GY+ + TG LW+ N D K+ FP + + G +
Sbjct: 653 GYVKAIDLKTGKELWKHRNGTVYDMTPVPLPFKVGFPTLGGPIGTAG----GVAFIAATG 708
Query: 157 KYQLALLSGSNGVQI--GTPLVKEDCDQMTGLNLTSPDTVIYV 197
L G+ G Q+ MT T YV
Sbjct: 709 DQYLRAYDGTGGKQLWQARLPAGGQATPMTY---TVAGGKQYV 748
>gnl|CDD|224437 COG1520, COG1520, FOG: WD40-like repeat [Function unknown].
Length = 370
Score = 30.2 bits (68), Expect = 4.4
Identities = 16/69 (23%), Positives = 28/69 (40%), Gaps = 6/69 (8%)
Query: 57 GGLIALDSVRPVELWRKTLNNVPKEVDCGLIDINLDGVLDCIVIAD-NGYLAVLSQATGN 115
G + AL+ + W L ++ ++ DG I + +G L L +TG
Sbjct: 78 GNIFALNPDTGLVKWSYPLLGAVAQLSGPILGS--DGK---IYVGSWDGKLYALDASTGT 132
Query: 116 LLWRKTNNG 124
L+W + G
Sbjct: 133 LVWSRNVGG 141
Score = 29.5 bits (66), Expect = 7.4
Identities = 20/94 (21%), Positives = 32/94 (34%), Gaps = 9/94 (9%)
Query: 57 GGLIALDSVRPVELWRKTLNNVPKEVDCGLIDINLDGVLDCIVIADNGYLAVLSQATGNL 116
G L ALD+ +W + + P + DG V D+G+L L+ TG L
Sbjct: 121 GKLYALDASTGTLVWSRNVGGSPYYASP---PVVGDGT--VYVGTDDGHLYALNADTGTL 175
Query: 117 LWRKTNNGYKDGKMKFPLIVDD----LTGDGVND 146
W + + + DG +
Sbjct: 176 KWTYETPAPLSLSIYGSPAIASGTVYVGSDGYDG 209
>gnl|CDD|236199 PRK08244, PRK08244, hypothetical protein; Provisional.
Length = 493
Score = 30.1 bits (68), Expect = 5.3
Identities = 24/85 (28%), Positives = 37/85 (43%), Gaps = 18/85 (21%)
Query: 354 VMFSPDGTPGPHIVNASQSDIIQLCHSNSCQPGTSLQEYSLLLADLDKDGSQDLISYLVT 413
V + PD PH +N + ++L S+ G S + YSLL G+ L+S+
Sbjct: 379 VHYEPDAEMPPHPLNGKRLPDLELTLSD----GESERLYSLL-----HKGTFLLLSF--- 426
Query: 414 YAGPDKSSDIQTWSLVSQIRVIRLE 438
S+ Q WS +RV+R
Sbjct: 427 ------GSEPQDWSRYPHVRVVRAS 445
>gnl|CDD|234102 TIGR03075, PQQ_enz_alc_DH, PQQ-dependent dehydrogenase,
methanol/ethanol family. This protein family has a
phylogenetic distribution very similar to that coenzyme
PQQ biosynthesis enzymes, as shown by partial
phylogenetic profiling. Genes in this family often are
found adjacent to the PQQ biosynthesis genes themselves.
An unusual, strained disulfide bond between adjacent Cys
residues contributes to PQQ-binding, as does a Trp
residue that is part of a PQQ enzyme repeat (see
pfam01011). Characterized members include the
dehydrogenase subunit of a membrane-anchored, three
subunit alcohol (ethanol) dehydrogenase of Gluconobacter
suboxydans, a homodimeric ethanol dehydrogenase in
Pseudomonas aeruginosa, and the large subunit of an
alpha2/beta2 heterotetrameric methanol dehydrogenase in
Methylobacterium extorquens.
Length = 526
Score = 30.0 bits (68), Expect = 5.9
Identities = 15/45 (33%), Positives = 20/45 (44%), Gaps = 4/45 (8%)
Query: 103 NGYLAVLSQATGNLLWRKTNNGYKDGKM--KFPLIVDD--LTGDG 143
+ L L TG ++W K N YK G PL+V +TG
Sbjct: 129 DARLVALDAKTGKVVWSKKNGDYKKGYTITAAPLVVKGKVITGIS 173
>gnl|CDD|236704 PRK10506, PRK10506, hypothetical protein; Provisional.
Length = 162
Score = 28.8 bits (65), Expect = 6.8
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 516 RVILYPTVRNLRDYLSWRQADAHINN 541
R L+ T + L D+L Q DA+ +N
Sbjct: 40 RQRLWQTAQQLLDFLLRLQEDANWHN 65
Score = 28.8 bits (65), Expect = 6.8
Identities = 10/26 (38%), Positives = 15/26 (57%)
Query: 719 RVILYPTVRNLRDYLSWRQADAHINN 744
R L+ T + L D+L Q DA+ +N
Sbjct: 40 RQRLWQTAQQLLDFLLRLQEDANWHN 65
>gnl|CDD|190827 pfam04002, RadC, RadC-like JAB domain. A family of proteins
present widely across the bacteria. This family was
named initially with reference to the E. coli radC102
mutation which suggested that RadC was involved in
repair of DNA lesions. However the relevant mutation has
subsequently been shown to be in recG, where radC is in
fact an allele of recG. In addition, a personal
communication from Claverys, J-P, et al, indicates a
total failure of all attempts to characterize a
radiation-related function for RadC in Streptococcus
pneumoniae, suggesting that it is not involved in repair
of DNA lesions, in recombination during transformation,
in gene conversion, nor in mismatch repair.
Computational analysis, however, provides a possible
function. The RadC-like family belong to the JAB
superfamily of metalloproteins. The domain shows fusions
to an N-terminal Helix-hairpin-Helix (HhH) domain in
most instances. Other domain combinations include
fusions to the anti-restriction module ArdC, the
DinG/RAD3-like superfamily II helicases and the
DNAG-like primase. In some bacteria, closely related
DinG/Rad3- like superfamily II helicases are fused to a
3'-5' exonuclease in the same position as the RadC-like
JAB domain. These conserved domain associations lead to
the hypothesis that the RadC-like JAB domains might
function as a nuclease.
Length = 123
Score = 27.9 bits (63), Expect = 10.0
Identities = 10/23 (43%), Positives = 12/23 (52%), Gaps = 3/23 (13%)
Query: 84 CGLIDINLDGVLDCIVIADNGYL 106
L+ I L LD I+I D GY
Sbjct: 96 GELLGIRL---LDHIIIGDGGYF 115
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
0.320 0.136 0.426
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 42,750,511
Number of extensions: 4150382
Number of successful extensions: 2984
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2971
Number of HSP's successfully gapped: 32
Length of query: 848
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 743
Effective length of database: 6,280,432
Effective search space: 4666360976
Effective search space used: 4666360976
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 63 (28.0 bits)