RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5349
(213 letters)
>gnl|CDD|233035 TIGR00585, mutl, DNA mismatch repair protein MutL. All proteins in
this family for which the functions are known are
involved in the process of generalized mismatch repair.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 312
Score = 205 bits (525), Expect = 3e-66
Identities = 77/195 (39%), Positives = 122/195 (62%), Gaps = 3/195 (1%)
Query: 1 MSINILPQSTIRQITTSQIITSVSTAVKELIENAIDAKATSIQINLMNQGLDLIEVKDDG 60
M+I LP + +I ++I ++ VKEL+EN++DA AT I + + GL LIEV D+G
Sbjct: 1 MTIKPLPPELVNKIAAGEVIERPASVVKELVENSLDAGATRIDVEIEEGGLKLIEVSDNG 60
Query: 61 SGIPTQDVPLICQAATTSKITDITDLDSLSSYGFRGEALNALCQIGEVSVTTKTNSDPVA 120
SGI +D+PL C+ TSKI DL+ + + GFRGEAL ++ + +++TTKT++
Sbjct: 61 SGIDKEDLPLACERHATSKIQSFEDLERIETLGFRGEALASISSVSRLTITTKTSAADGL 120
Query: 121 SMYKFSHTGEVTSTQPSHFPNGTTVSVKNLFHNLPVRKQYLSSKNRMLEELRKVERVVKC 180
+ G + S +P+ P GTTV V++LF+NLPVR+++L S + E RK+ V++
Sbjct: 121 AYQALLEGGMIESIKPAPRPVGTTVEVRDLFYNLPVRRKFLKSPKK---EFRKILDVLQR 177
Query: 181 LSLIHCKLRVTLTHN 195
+LIH + +LTH+
Sbjct: 178 YALIHPDISFSLTHD 192
>gnl|CDD|223400 COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA
replication, recombination, and repair].
Length = 638
Score = 213 bits (545), Expect = 6e-66
Identities = 67/194 (34%), Positives = 109/194 (56%), Gaps = 3/194 (1%)
Query: 2 SINILPQSTIRQITTSQIITSVSTAVKELIENAIDAKATSIQINLMNQGLDLIEVKDDGS 61
I LP + QI ++I ++ VKEL+EN++DA AT I I + GL LI V+D+GS
Sbjct: 3 KIRQLPPDLVNQIAAGEVIERPASVVKELVENSLDAGATRIDIEVEGGGLKLIRVRDNGS 62
Query: 62 GIPTQDVPLICQAATTSKITDITDLDSLSSYGFRGEALNALCQIGEVSVTTKTNSDPVAS 121
GI +D+PL TSKI + DL + + GFRGEAL ++ + +++T++T +
Sbjct: 63 GIDKEDLPLALLRHATSKIASLEDLFRIRTLGFRGEALASIASVSRLTITSRTAEASEGT 122
Query: 122 MYKFSHTGEVTSTQPSHFPNGTTVSVKNLFHNLPVRKQYLSSKNRMLEELRKVERVVKCL 181
G + +P+ P GTTV V++LF+N P R+++L S+ E + ++
Sbjct: 123 QIYAEGGGMEVTVKPAAHPVGTTVEVRDLFYNTPARRKFLKSEKT---EFGHITELINRY 179
Query: 182 SLIHCKLRVTLTHN 195
+L H + +L+HN
Sbjct: 180 ALAHPDISFSLSHN 193
>gnl|CDD|234630 PRK00095, mutL, DNA mismatch repair protein; Reviewed.
Length = 617
Score = 167 bits (425), Expect = 1e-48
Identities = 72/195 (36%), Positives = 113/195 (57%), Gaps = 4/195 (2%)
Query: 1 MSINILPQSTIRQITTSQIITSVSTAVKELIENAIDAKATSIQINLMNQGLDLIEVKDDG 60
M I +LP QI +++ ++ VKEL+ENA+DA AT I I + GL LI V+D+G
Sbjct: 1 MPIQLLPPQLANQIAAGEVVERPASVVKELVENALDAGATRIDIEIEEGGLKLIRVRDNG 60
Query: 61 SGIPTQDVPLICQAATTSKITDITDLDSLSSYGFRGEALNALCQIGEVSVTTKTNSDPVA 120
GI +D+ L TSKI + DL+++ + GFRGEAL ++ + +++T++T
Sbjct: 61 CGISKEDLALALARHATSKIASLDDLEAIRTLGFRGEALPSIASVSRLTLTSRTADAAEG 120
Query: 121 SMYKFSHTGEVTSTQPSHFPNGTTVSVKNLFHNLPVRKQYLSSKNRMLEELRKVERVVKC 180
+ GE+ +P+ P GTT+ V++LF N P R+++L S+ EL ++ VV
Sbjct: 121 WQIVY-EGGEIVEVKPAAHPVGTTIEVRDLFFNTPARRKFLKSEKT---ELGHIDDVVNR 176
Query: 181 LSLIHCKLRVTLTHN 195
L+L H + TLTHN
Sbjct: 177 LALAHPDVAFTLTHN 191
>gnl|CDD|222246 pfam13589, HATPase_c_3, Histidine kinase-, DNA gyrase B-, and
HSP90-like ATPase. This family represents,
additionally, the structurally related ATPase domains of
histidine kinase, DNA gyrase B and HSP90.
Length = 134
Score = 60.8 bits (148), Expect = 4e-12
Identities = 27/100 (27%), Positives = 56/100 (56%), Gaps = 3/100 (3%)
Query: 22 SVSTAVKELIENAIDAKATSIQINL-MNQGLDLIEVKDDGSGIPTQDVPLICQAATTSKI 80
++ A+ ELI+N+IDA AT+++I++ ++G D I ++D+G G+ +++ + +SK
Sbjct: 2 TLEDAIAELIDNSIDADATNVKISIDPDRGEDGISIEDNGGGMSYEELRNALKLGRSSK- 60
Query: 81 TDITDLDSLSSYGFRGEALNALCQIGEVSVTTKTNSDPVA 120
D +L G + L +L +++VT+K +
Sbjct: 61 EGERDSTTLGRKGIGMK-LASLSLGRKLTVTSKKEGESST 99
>gnl|CDD|238030 cd00075, HATPase_c, Histidine kinase-like ATPases; This family
includes several ATP-binding proteins for example:
histidine kinase, DNA gyrase B, topoisomerases, heat
shock protein HSP90, phytochrome-like ATPases and DNA
mismatch repair proteins.
Length = 103
Score = 48.4 bits (116), Expect = 8e-08
Identities = 23/100 (23%), Positives = 39/100 (39%), Gaps = 19/100 (19%)
Query: 26 AVKELIENAIDA---KATSIQINLMNQGLDL-IEVKDDGSGIPTQDVPLICQAATTSKIT 81
+ L+ NAI I I++ G L I V+D+G GIP +D+ I +
Sbjct: 4 VLLNLLSNAIKHTPEGGGRITISVERDGDHLEIRVEDNGPGIPEEDLERIFER------- 56
Query: 82 DITDLDSLSSYGFRGEALNALCQI------GEVSVTTKTN 115
+D G G L ++ + G + V ++
Sbjct: 57 -FSDGSRSRKGGGTGLGL-SIVKKLVELHGGRIEVESEPG 94
>gnl|CDD|217081 pfam02518, HATPase_c, Histidine kinase-, DNA gyrase B-, and
HSP90-like ATPase. This family represents the
structurally related ATPase domains of histidine
kinase, DNA gyrase B and HSP90.
Length = 111
Score = 44.6 bits (106), Expect = 2e-06
Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 3/57 (5%)
Query: 26 AVKELIENAIDA--KATSIQINLMNQGLDL-IEVKDDGSGIPTQDVPLICQAATTSK 79
+ L++NAI I++ L G L I V+D+G GIP +D+P I + +
Sbjct: 9 VLSNLLDNAIKHAPAGGEIEVTLERDGGRLRITVEDNGIGIPPEDLPKIFEPFFRTD 65
>gnl|CDD|214643 smart00387, HATPase_c, Histidine kinase-like ATPases. Histidine
kinase-, DNA gyrase B-, phytochrome-like ATPases.
Length = 111
Score = 42.3 bits (100), Expect = 1e-05
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 3/57 (5%)
Query: 26 AVKELIENAIDA--KATSIQINLMNQGLDL-IEVKDDGSGIPTQDVPLICQAATTSK 79
+ L++NAI + I + L G + I V+D+G GIP +D+ I + +
Sbjct: 9 VLSNLLDNAIKYTPEGGRITVTLERDGDHVEITVEDNGPGIPPEDLEKIFEPFFRTD 65
>gnl|CDD|235246 PRK04184, PRK04184, DNA topoisomerase VI subunit B; Validated.
Length = 535
Score = 39.9 bits (94), Expect = 6e-04
Identities = 19/59 (32%), Positives = 37/59 (62%), Gaps = 9/59 (15%)
Query: 22 SVSTAVKELIENAIDAKATS-------IQINLMNQGLDL--IEVKDDGSGIPTQDVPLI 71
++ T VKEL++N++DA + I+I +++G D + V+D+G GIP +++P +
Sbjct: 36 ALYTTVKELVDNSLDACEEAGILPDIKIEIKRVDEGKDHYRVTVEDNGPGIPPEEIPKV 94
>gnl|CDD|224307 COG1389, COG1389, DNA topoisomerase VI, subunit B [DNA
replication, recombination, and repair].
Length = 538
Score = 38.9 bits (91), Expect = 0.001
Identities = 17/57 (29%), Positives = 32/57 (56%), Gaps = 7/57 (12%)
Query: 20 ITSVSTAVKELIENAIDAKATS-------IQINLMNQGLDLIEVKDDGSGIPTQDVP 69
I S++T V EL+ N++DA + ++I + + + V+D+G GIP + +P
Sbjct: 34 IRSLTTTVHELVTNSLDACEEAGILPDIKVEIERIGKDHYKVIVEDNGPGIPEEQIP 90
>gnl|CDD|236839 PRK11086, PRK11086, sensory histidine kinase DcuS; Provisional.
Length = 542
Score = 38.4 bits (90), Expect = 0.002
Identities = 18/65 (27%), Positives = 28/65 (43%), Gaps = 7/65 (10%)
Query: 9 STIRQITTSQIITSVSTAVKELIENAIDA------KATSIQINLMNQGLDLIEVKDDGSG 62
S + + + T + LIENA++A S+ ++ N L EV DDG G
Sbjct: 420 SQLPDSGDEDQVHELITILGNLIENALEAVGGEEGGEISVSLHYRNGWLH-CEVSDDGPG 478
Query: 63 IPTQD 67
I +
Sbjct: 479 IAPDE 483
>gnl|CDD|223265 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), B subunit [DNA replication,
recombination, and repair].
Length = 635
Score = 38.3 bits (90), Expect = 0.002
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 6/43 (13%)
Query: 27 VKELIENAIDAK----ATSIQINLMNQGLDLIEVKDDGSGIPT 65
V E+++N+ID A I + L G I V+D+G GIP
Sbjct: 41 VWEVVDNSIDEALAGYADRIDVTLHEDGS--ISVEDNGRGIPV 81
>gnl|CDD|223715 COG0642, BaeS, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 336
Score = 37.4 bits (86), Expect = 0.003
Identities = 14/44 (31%), Positives = 22/44 (50%), Gaps = 2/44 (4%)
Query: 30 LIENAIDA-KATSIQINLMNQGLDL-IEVKDDGSGIPTQDVPLI 71
L+ NAI I I++ + I V+D G GIP +++ I
Sbjct: 236 LLSNAIKYTPGGEITISVRQDDEQVTISVEDTGPGIPEEELERI 279
>gnl|CDD|225827 COG3290, CitA, Signal transduction histidine kinase regulating
citrate/malate metabolism [Signal transduction
mechanisms].
Length = 537
Score = 36.5 bits (85), Expect = 0.007
Identities = 25/84 (29%), Positives = 44/84 (52%), Gaps = 6/84 (7%)
Query: 2 SINILPQSTIRQITTSQIITSVSTAVKELIENAIDAKAT-----SIQINLMNQGLDL-IE 55
S+ I P S + Q+ + + T + LI+NA++A I+++L ++G +L IE
Sbjct: 407 SLIIDPNSQLPQLPSELQPHDLVTILGNLIDNALEALLAPEENKEIELSLSDRGDELVIE 466
Query: 56 VKDDGSGIPTQDVPLICQAATTSK 79
V D G GIP + I + ++K
Sbjct: 467 VADTGPGIPPEVRDKIFEKGVSTK 490
>gnl|CDD|235501 PRK05559, PRK05559, DNA topoisomerase IV subunit B; Reviewed.
Length = 631
Score = 35.8 bits (84), Expect = 0.011
Identities = 17/47 (36%), Positives = 27/47 (57%), Gaps = 6/47 (12%)
Query: 27 VKELIENAID-AKA---TSIQINLMNQGLDLIEVKDDGSGIPTQDVP 69
V+E+I+N++D A A I++ L G + V+D+G GIP P
Sbjct: 42 VQEVIDNSVDEALAGHGKRIEVTLHADGS--VSVRDNGRGIPVGIHP 86
>gnl|CDD|214659 smart00433, TOP2c, TopoisomeraseII. Eukaryotic DNA topoisomerase
II, GyrB, ParE.
Length = 594
Score = 34.5 bits (80), Expect = 0.035
Identities = 13/43 (30%), Positives = 25/43 (58%), Gaps = 6/43 (13%)
Query: 27 VKELIENAIDAK----ATSIQINLMNQGLDLIEVKDDGSGIPT 65
V E+++NA D +I++ + ++ + I V+D+G GIP
Sbjct: 6 VDEIVDNAADEALAGYMDTIKVTI-DKD-NSISVEDNGRGIPV 46
>gnl|CDD|226369 COG3851, UhpB, Signal transduction histidine kinase,
glucose-6-phosphate specific [Signal transduction
mechanisms].
Length = 497
Score = 34.0 bits (78), Expect = 0.055
Identities = 16/41 (39%), Positives = 25/41 (60%), Gaps = 2/41 (4%)
Query: 27 VKELIENAID-AKATSIQINLMNQGLDLI-EVKDDGSGIPT 65
+EL+ N A A+++ I L Q L+ E++DDGSG+P
Sbjct: 415 CQELLNNICKHADASAVTIQLWQQDERLMLEIEDDGSGLPP 455
>gnl|CDD|185013 PRK15053, dpiB, sensor histidine kinase DpiB; Provisional.
Length = 545
Score = 33.7 bits (77), Expect = 0.062
Identities = 21/73 (28%), Positives = 37/73 (50%), Gaps = 7/73 (9%)
Query: 1 MSINILPQSTIRQITTSQIITSVSTAVKELIENAIDAKATS------IQINLMNQGLD-L 53
+ + I+P S + Q+ T + V L++NA +A S +++ L ++G D +
Sbjct: 411 LKMVIVPGSQLSQLPPGLDSTEFAAIVGNLLDNAFEASLRSDEGNKIVELFLSDEGDDVV 470
Query: 54 IEVKDDGSGIPTQ 66
IEV D G G+P
Sbjct: 471 IEVADQGCGVPES 483
>gnl|CDD|233250 TIGR01052, top6b, DNA topoisomerase VI, B subunit. This model
describes DNA topoisomerase VI, an archaeal type II DNA
topoisomerase (DNA gyrase) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 488
Score = 33.3 bits (76), Expect = 0.081
Identities = 18/57 (31%), Positives = 33/57 (57%), Gaps = 7/57 (12%)
Query: 20 ITSVSTAVKELIENAIDAKATS-----IQINLMNQGLD--LIEVKDDGSGIPTQDVP 69
I S++T + EL+ N++DA + I++ + G D + V+D+G GIP + +P
Sbjct: 26 IRSLTTVIHELVTNSLDACEEAGILPDIKVEIEKIGKDHYKVTVEDNGPGIPEEYIP 82
>gnl|CDD|179626 PRK03660, PRK03660, anti-sigma F factor; Provisional.
Length = 146
Score = 31.8 bits (73), Expect = 0.10
Identities = 20/67 (29%), Positives = 32/67 (47%), Gaps = 10/67 (14%)
Query: 20 ITSVSTAVKELIENAI-------DAKATSIQINLMNQGLDLIEVKDDGSGIPTQDVPLIC 72
+T + TAV E + NAI I++ + + L+ I V+D+G GI D+
Sbjct: 37 LTEIKTAVSEAVTNAIIHGYENNPDGVVYIEVEIEEEELE-ITVRDEGKGIE--DIEEAM 93
Query: 73 QAATTSK 79
Q T+K
Sbjct: 94 QPLYTTK 100
>gnl|CDD|235542 PRK05644, gyrB, DNA gyrase subunit B; Validated.
Length = 638
Score = 32.8 bits (76), Expect = 0.13
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 6/43 (13%)
Query: 27 VKELIENAID-AKA---TSIQINLMNQGLDLIEVKDDGSGIPT 65
V E+++N+ID A A I++ + G I V D+G GIP
Sbjct: 42 VYEIVDNSIDEALAGYCDHIEVTINEDGS--ITVTDNGRGIPV 82
>gnl|CDD|226368 COG3850, NarQ, Signal transduction histidine kinase,
nitrate/nitrite-specific [Signal transduction
mechanisms].
Length = 574
Score = 32.7 bits (75), Expect = 0.14
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 27 VKELIENAID-AKATSIQINLMNQGLDL-IEVKDDGSGIPTQDVP 69
V+E + NAI A+A+ I++ + + + V+D+G GI P
Sbjct: 486 VREALSNAIKHAQASEIKVTVSQNDGQVTLTVEDNGVGIDEAAEP 530
>gnl|CDD|237841 PRK14867, PRK14867, DNA topoisomerase VI subunit B; Provisional.
Length = 659
Score = 32.5 bits (74), Expect = 0.14
Identities = 18/57 (31%), Positives = 33/57 (57%), Gaps = 7/57 (12%)
Query: 20 ITSVSTAVKELIENAIDAKATS-----IQINLMNQGLDL--IEVKDDGSGIPTQDVP 69
+ S++T + EL+ N++DA + I++ + G D + V+D+G GIP + VP
Sbjct: 34 LRSMTTIIHELVTNSLDACEEAEILPDIKVEIEKLGSDHYKVAVEDNGPGIPPEFVP 90
>gnl|CDD|234074 TIGR02966, phoR_proteo, phosphate regulon sensor kinase PhoR.
Members of this protein family are the regulatory
histidine kinase PhoR associated with the phosphate ABC
transporter in most Proteobacteria. Related proteins
from Gram-positive organisms are not included in this
model. The phoR gene usually is adjacent to the response
regulator phoB gene (TIGR02154) [Signal transduction,
Two-component systems].
Length = 333
Score = 31.4 bits (72), Expect = 0.27
Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 5/48 (10%)
Query: 26 AVKELIENAI----DAKATSIQINLMNQGLDLIEVKDDGSGIPTQDVP 69
A L+ NAI + +++ G + V D G GI + +P
Sbjct: 233 AFSNLVSNAIKYTPEGGTITVRWRRDGGGAEF-SVTDTGIGIAPEHLP 279
>gnl|CDD|233254 TIGR01059, gyrB, DNA gyrase, B subunit. This model describes the
common type II DNA topoisomerase (DNA gyrase). Two
apparently independently arising families, one in the
Proteobacteria and one in Gram-positive lineages, are
both designated toposisomerase IV. Proteins scoring
above the noise cutoff for this model and below the
trusted cutoff for topoisomerase IV models probably
should be designated GyrB [DNA metabolism, DNA
replication, recombination, and repair].
Length = 654
Score = 31.6 bits (72), Expect = 0.28
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 6/44 (13%)
Query: 27 VKELIENAIDAK----ATSIQINLMNQGLDLIEVKDDGSGIPTQ 66
V E+++N+ID +I + + + G + V+D+G GIP
Sbjct: 35 VYEVVDNSIDEAMAGYCDTINVTINDDGS--VTVEDNGRGIPVD 76
>gnl|CDD|236701 PRK10490, PRK10490, sensor protein KdpD; Provisional.
Length = 895
Score = 31.5 bits (72), Expect = 0.35
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 30 LIENAIDAKATSIQINL----MNQGLDLIEVKDDGSGIPTQDVPLI 71
L+ENA+ +I + + L ++V D+G GIP LI
Sbjct: 786 LLENAVKYAGAQAEIGIDAHVEGERLQ-LDVWDNGPGIPPGQEQLI 830
>gnl|CDD|226951 COG4585, COG4585, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 365
Score = 30.1 bits (68), Expect = 0.84
Identities = 14/41 (34%), Positives = 22/41 (53%), Gaps = 2/41 (4%)
Query: 26 AVKELIENAID-AKATSIQINL-MNQGLDLIEVKDDGSGIP 64
V+E + NAI A+AT +++ L +EV D+G G
Sbjct: 283 IVQEALTNAIRHAQATEVRVTLERTDDELRLEVIDNGVGFD 323
>gnl|CDD|237860 PRK14939, gyrB, DNA gyrase subunit B; Provisional.
Length = 756
Score = 30.1 bits (69), Expect = 0.85
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 10/45 (22%)
Query: 27 VKELIENAID------AKATSIQINLMNQGLDLIEVKDDGSGIPT 65
V E+++NAID ++ I+ + V D+G GIPT
Sbjct: 42 VYEVVDNAIDEALAGHCDDITVTIHADGS----VSVSDNGRGIPT 82
>gnl|CDD|225115 COG2205, KdpD, Osmosensitive K+ channel histidine kinase [Signal
transduction mechanisms].
Length = 890
Score = 30.3 bits (69), Expect = 0.87
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 30 LIENAID--AKATSIQINLMNQGLDL-IEVKDDGSGIPTQDVPLI 71
L+ENA+ + I+IN + ++ V D+G GIP ++ I
Sbjct: 783 LLENALKYAPPGSEIRINAGVERENVVFSVIDEGPGIPEGELERI 827
>gnl|CDD|236724 PRK10604, PRK10604, sensor protein RstB; Provisional.
Length = 433
Score = 30.0 bits (68), Expect = 1.0
Identities = 12/43 (27%), Positives = 25/43 (58%), Gaps = 1/43 (2%)
Query: 26 AVKELIENAIDAKATSIQINLMNQG-LDLIEVKDDGSGIPTQD 67
+ L+ NA+ + ++++L+ G + V+DDG GIP ++
Sbjct: 323 VLDNLLNNALRYAHSRVRVSLLLDGNQACLIVEDDGPGIPPEE 365
>gnl|CDD|236800 PRK10935, PRK10935, nitrate/nitrite sensor protein NarQ;
Provisional.
Length = 565
Score = 29.8 bits (68), Expect = 1.0
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 27 VKELIENAID-AKATSIQIN--LMNQGLDLIEVKDDGSGIPTQDVP 69
++E NAI A A+ I ++ G + ++DDG GI P
Sbjct: 476 IREATLNAIKHANASEIAVSCVTNPDGEHTVSIRDDGIGIGELKEP 521
>gnl|CDD|236846 PRK11100, PRK11100, sensory histidine kinase CreC; Provisional.
Length = 475
Score = 29.8 bits (68), Expect = 1.0
Identities = 13/42 (30%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 26 AVKELIENAID--AKATSIQINL-MNQGLDLIEVKDDGSGIP 64
A+ L++NAID + +I ++ ++ + V+D G GIP
Sbjct: 372 ALGNLLDNAIDFSPEGGTITLSAEVDGEQVALSVEDQGPGIP 413
>gnl|CDD|236532 PRK09470, cpxA, two-component sensor protein; Provisional.
Length = 461
Score = 29.9 bits (68), Expect = 1.1
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 26 AVKELIENAIDAKATSIQIN--LMNQGLDLIEVKDDGSGIPTQD 67
A++ ++ NA+ T I++ + GL I V DDG G+P ++
Sbjct: 357 ALENIVRNALRYSHTKIEVAFSVDKDGL-TITVDDDGPGVPEEE 399
>gnl|CDD|236531 PRK09467, envZ, osmolarity sensor protein; Provisional.
Length = 435
Score = 29.5 bits (67), Expect = 1.3
Identities = 12/49 (24%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 22 SVSTAVKELIENAIDAKATSIQINL-MNQGLDLIEVKDDGSGIPTQDVP 69
++ A+ L+ NA I+++ +V+DDG GIP + +
Sbjct: 331 AIKRALANLVVNAARYGNGWIKVSSGTEGKRAWFQVEDDGPGIPPEQLK 379
>gnl|CDD|226434 COG3920, COG3920, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 221
Score = 28.8 bits (65), Expect = 1.6
Identities = 15/47 (31%), Positives = 21/47 (44%), Gaps = 8/47 (17%)
Query: 26 AVKELIENAI-----DAKATSIQINL---MNQGLDLIEVKDDGSGIP 64
V EL+ NA+ I+I L + G L+ V D+G G P
Sbjct: 126 IVHELVTNALKHAFLSRPGGEIRITLSREGDGGRFLLTVWDEGGGPP 172
>gnl|CDD|176851 cd00177, START, Lipid-binding START domain of mammalian
STARD1-STARD15 and related proteins. This family
includes the steroidogenic acute regulatory protein
(StAR)-related lipid transfer (START) domains of
mammalian STARD1-STARD15, and related domains, such as
the START domain of the Arabidopsis homeobox protein
GLABRA 2. The mammalian STARDs are grouped into 8
subfamilies. This family belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket. For some members of this family, specific lipids
that bind in this pocket are known; these include
cholesterol (STARD1/STARD3/ STARD4/STARD5),
25-hydroxycholesterol (STARD5), phosphatidylcholine
(STARD2/ STARD7/STARD10), phosphatidylethanolamine
(STARD10) and ceramides (STARD11). The START domain is
found either alone or in association with other domains.
Mammalian STARDs participate in the control of various
cellular processes including lipid trafficking between
intracellular compartments, lipid metabolism, and
modulation of signaling events. Mutation or altered
expression of STARDs is linked to diseases such as
cancer, genetic disorders, and autoimmune disease. The
Arabidopsis homeobox protein GLABRA 2 suppresses root
hair formation in hairless epidermal root cells.
Length = 193
Score = 28.5 bits (64), Expect = 1.9
Identities = 15/88 (17%), Positives = 33/88 (37%), Gaps = 15/88 (17%)
Query: 102 LCQIGEVSVTTKTNSDPVASMYKFSHTGEVTSTQPSHFPNGTTVSVKNLFHNLPVRKQYL 161
+ + V + TK D + K + Q V L ++ +RK++
Sbjct: 20 VKEKDGVKIYTKPYEDSGLKLLKAEGVIPASPEQ-----------VFELLMDIDLRKKW- 67
Query: 162 SSKNRMLEELRKVERVVKCLSLIHCKLR 189
++ EE +E + + +I+ K +
Sbjct: 68 ---DKNFEEFEVIEEIDEHTDIIYYKTK 92
>gnl|CDD|237842 PRK14868, PRK14868, DNA topoisomerase VI subunit B; Provisional.
Length = 795
Score = 29.0 bits (65), Expect = 2.3
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 8/54 (14%)
Query: 25 TAVKELIENAIDAKATS-------IQINLMNQGLDLIEVKDDGSGIPTQDVPLI 71
TAVKE ++NA+DA + ++I + L+ V+D+G GI + +P +
Sbjct: 49 TAVKEAVDNALDATEEAGILPDIYVEIEEVGDYYRLV-VEDNGPGITKEQIPKV 101
>gnl|CDD|227335 COG5002, VicK, Signal transduction histidine kinase [Signal
transduction mechanisms].
Length = 459
Score = 28.2 bits (63), Expect = 3.3
Identities = 12/45 (26%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 30 LIENAI--DAKATSIQINLMNQGLDL-IEVKDDGSGIPTQDVPLI 71
+I NA+ I +++ + + I + D G GIP +D+ I
Sbjct: 350 IISNALKYSPDGGRITVSVKQRETWVEISISDQGLGIPKEDLEKI 394
>gnl|CDD|131984 TIGR02938, nifL_nitrog, nitrogen fixation negative regulator NifL.
NifL is a modulator of the nitrogen fixation positive
regulator protein NifA, and is therefore a negative
regulator. It binds NifA. NifA and NifL are encoded by
adjacent genes [Central intermediary metabolism,
Nitrogen fixation, Regulatory functions, Protein
interactions].
Length = 494
Score = 28.3 bits (63), Expect = 3.4
Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 9/46 (19%)
Query: 27 VKELIENAIDAKATS--------IQINLMNQGLDLIEVKDDGSGIP 64
K L++NAI+A I L L ++ + D G GIP
Sbjct: 392 FKALVDNAIEAMNIKGWKRRELSITTALNGD-LIVVSILDSGPGIP 436
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 28.1 bits (63), Expect = 4.6
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 9/46 (19%)
Query: 29 ELIENAIDAKA--------TSIQINLMNQGLDLIEVKDDGSGIPTQ 66
E++ NA D KA T I++ +++ I V +DG GIP Q
Sbjct: 64 EILVNAADNKARDKGGHRMTYIKVT-IDEENGEISVYNDGEGIPVQ 108
>gnl|CDD|220749 pfam10428, SOG2, RAM signalling pathway protein. SOG2 proteins in
Saccharomyces cerevisiae are involved in cell separation
and cytokinesis.
Length = 419
Score = 27.4 bits (61), Expect = 5.8
Identities = 19/74 (25%), Positives = 30/74 (40%), Gaps = 12/74 (16%)
Query: 1 MSINILPQSTIRQITTSQIITSVSTA--------VKELIENAIDAKATSIQINLMNQGLD 52
M++ +LPQ Q + S I ++ S KELIE A + + + L
Sbjct: 290 MALRVLPQ-LTEQFSKSLIASTTSRNITPSLVAKWKELIEKCRVALQVTEA---LRERLS 345
Query: 53 LIEVKDDGSGIPTQ 66
I+ K+ I Q
Sbjct: 346 TIKTKEPYGTIREQ 359
>gnl|CDD|131174 TIGR02119, panF, sodium/pantothenate symporter. Pantothenate
(vitamin B5) is a precursor of coenzyme A and is made
from aspartate and 2-oxoisovalerate in most bacteria
with completed genome sequences. However, some pathogens
must import pantothenate. This model describes PanF, a
sodium/pantothenate symporter, from a larger family of
Sodium/substrate symporters (pfam00474). Several species
that have this transporter appear to lack all enzymes of
pantothenate biosynthesis, namely Haemophilus
influenzae, Pasteurella multocida, Fusobacterium
nucleatum, and Borrelia burgdorferi [Biosynthesis of
cofactors, prosthetic groups, and carriers, Pantothenate
and coenzyme A, Transport and binding proteins, Other].
Length = 471
Score = 27.4 bits (61), Expect = 5.9
Identities = 14/48 (29%), Positives = 24/48 (50%)
Query: 7 PQSTIRQITTSQIITSVSTAVKELIENAIDAKATSIQINLMNQGLDLI 54
P + I S ++ S ST +K+L N I +A +I ++ + LI
Sbjct: 327 PMAAIMSTVNSLLLQSSSTIIKDLYLNYIPKEAKESKIKKISMCITLI 374
>gnl|CDD|130130 TIGR01058, parE_Gpos, DNA topoisomerase IV, B subunit,
Gram-positive. Operationally, topoisomerase IV is a
type II topoisomerase required for the decatenation
step of chromosome segregation. Not every bacterium has
both a topo II and a topo IV. The topo IV families of
the Gram-positive bacteria and the Gram-negative
bacteria appear not to represent a single clade among
the type II topoisomerases, and are represented by
separate models for this reason [DNA metabolism, DNA
replication, recombination, and repair].
Length = 637
Score = 27.5 bits (61), Expect = 6.3
Identities = 15/45 (33%), Positives = 25/45 (55%), Gaps = 10/45 (22%)
Query: 27 VKELIENAID------AKATSIQINLMNQGLDLIEVKDDGSGIPT 65
V E+++N++D A ++ ++ N I V+DDG GIPT
Sbjct: 39 VWEIVDNSVDEVLAGYADNITVTLHKDNS----ITVQDDGRGIPT 79
>gnl|CDD|236835 PRK11069, recC, exonuclease V subunit gamma; Provisional.
Length = 1122
Score = 27.6 bits (62), Expect = 6.5
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 86 LDSLSSYGFRGEALNAL 102
LD LS Y + LNAL
Sbjct: 872 LDGLSRYQLNQQLLNAL 888
>gnl|CDD|200496 cd11235, Sema_semaphorin, The Sema domain, a protein interacting
module, of semaphorins. Semaphorins are regulator
molecules in the development of the nervous system and
in axonal guidance. They also play important roles in
other biological processes, such as angiogenesis, immune
regulation, respiration systems and cancer. They can be
divided into 7 classes. Vertebrates have members in
classes 3-7, whereas classes 1 and 2 are known only in
invertebrates. Class 2 and 3 semaphorins are secreted
proteins; classes 1 and 4 through 6 are transmembrane
proteins; and class 7 is membrane associated via
glycosylphosphatidylinositol (GPI) linkage. The
semaphorins exert their function through their
receptors, the neuropilin and plexin families. The Sema
domain is located at the N-terminus and contains four
disulfide bonds formed by eight conserved cysteine
residues. It serves as a receptor-recognition and
-binding module.
Length = 437
Score = 27.4 bits (61), Expect = 6.6
Identities = 13/38 (34%), Positives = 18/38 (47%)
Query: 128 TGEVTSTQPSHFPNGTTVSVKNLFHNLPVRKQYLSSKN 165
GE+ S + F V + L HN P+R +Y SK
Sbjct: 121 DGELYSGTSADFLGTDPVIYRTLGHNPPLRTEYHDSKW 158
>gnl|CDD|182947 PRK11073, glnL, nitrogen regulation protein NR(II); Provisional.
Length = 348
Score = 27.0 bits (60), Expect = 7.2
Identities = 10/30 (33%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 40 TSIQINLMNQGLDL---IEVKDDGSGIPTQ 66
T+ Q+ L + L I+++D+G GIP
Sbjct: 266 TAFQLTLHGERYRLAARIDIEDNGPGIPPH 295
>gnl|CDD|233031 TIGR00577, fpg, formamidopyrimidine-DNA glycosylase (fpg). All
proteins in the FPG family with known functions are
FAPY-DNA glycosylases that function in base excision
repair. Homologous to endonuclease VIII (nei). This
family is based on the phylogenomic analysis of JA Eisen
(1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 272
Score = 26.9 bits (60), Expect = 7.3
Identities = 9/39 (23%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 5 ILPQSTIRQITTSQIITSVSTAVKELIENAIDAKATSIQ 43
I P+ ++ + + A+KE++ AI+ T+I+
Sbjct: 185 IHPERLANSLSKEEC-ELLHRAIKEVLRKAIEMGGTTIR 222
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
0.317 0.130 0.369
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,041,788
Number of extensions: 877348
Number of successful extensions: 874
Number of sequences better than 10.0: 1
Number of HSP's gapped: 850
Number of HSP's successfully gapped: 56
Length of query: 213
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 120
Effective length of database: 6,812,680
Effective search space: 817521600
Effective search space used: 817521600
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 (21.7 bits)
S2: 57 (25.6 bits)