RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2984
(228 letters)
>gnl|CDD|211398 cd11560, W2_eIF5C_like, C-terminal W2 domain of the eukaryotic
translation initiation factor 5C and similar proteins.
eIF5C appears to be essential for the initiation of
protein translation; its actual function, and
specifically that of the C-terminal W2 domain, are not
well understood. The Drosophila ortholog, kra
(krasavietz) or exba (extra bases), may be involved in
translational inhibition in neural development. The
structure of this C-terminal domain resembles that of a
set of concatenated HEAT repeats.
Length = 194
Score = 99.6 bits (249), Expect = 5e-26
Identities = 36/79 (45%), Positives = 58/79 (73%)
Query: 2 EFVPPNKRSDEYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVA 61
EF PPNKR++E+F F+E+GL ++V+ + QASQE KKELQ++L+E I+E +K+I+A
Sbjct: 1 EFFPPNKRTEEHFAEHFKEEGLDELVEFYRKQASQEIKKELQQELKEMIAEEEPVKEIIA 60
Query: 62 DIREIANKHCIPDQELIVL 80
++E K +P+ E++ L
Sbjct: 61 AVKEQMKKSSLPEHEVVGL 79
>gnl|CDD|215225 PLN02401, PLN02401, diacylglycerol o-acyltransferase.
Length = 446
Score = 97.1 bits (242), Expect = 2e-23
Identities = 39/94 (41%), Positives = 62/94 (65%), Gaps = 2/94 (2%)
Query: 120 RHLYKPLVEQGYSRLTASSLVFFISAFMHEYLVSVPLRTYKIWAFMGMMGQIPLSMLSRH 179
RH+Y P + G S+ A + FF+SA HE ++VP +K+WAF+G+M Q+PL ++ +
Sbjct: 345 RHIYFPCLRNGISKGVAILIAFFVSAVFHELCIAVPCHMFKLWAFLGIMFQVPLVFITNY 404
Query: 180 VEKKYGPRW-GNIIVWSSL-ILGQPLCIMMYYHD 211
++ K+ GN+I W ILGQP+C+++YYHD
Sbjct: 405 LQNKFKSSMVGNMIFWFFFCILGQPMCVLLYYHD 438
>gnl|CDD|178780 PLN03242, PLN03242, diacylglycerol o-acyltransferase; Provisional.
Length = 410
Score = 92.9 bits (231), Expect = 4e-22
Identities = 35/91 (38%), Positives = 59/91 (64%), Gaps = 2/91 (2%)
Query: 120 RHLYKPLVEQGYSRLTASSLVFFISAFMHEYLVSVPLRTYKIWAFMGMMGQIPLSMLSRH 179
RH+Y P + G + A +VFFISA HE ++VP + WAF+G+M Q+PL ++++
Sbjct: 320 RHVYFPCLRLGMPKQLAILVVFFISAVFHEVCIAVPCHMIRGWAFLGIMFQVPLVLVTKV 379
Query: 180 VEKKY-GPRWGNIIVWSSL-ILGQPLCIMMY 208
+++K+ GN+I W I+GQP+C+++Y
Sbjct: 380 LQRKFPSSMVGNMIFWFFFCIVGQPMCVLLY 410
>gnl|CDD|227389 COG5056, ARE1, Acyl-CoA cholesterol acyltransferase [Lipid
metabolism].
Length = 512
Score = 59.8 bits (145), Expect = 2e-10
Identities = 26/94 (27%), Positives = 45/94 (47%), Gaps = 2/94 (2%)
Query: 120 RHLYKPLVEQ-GYSRLTASSLVFFISAFMHEYLVSVPLRTYKIWAFMGMMGQIPLSMLSR 178
RH+Y + S+ A+ FFIS+ +HE ++S+ + + + + QIPL L+
Sbjct: 420 RHVYHSSISGFKLSKSQATLFTFFISSVVHELVMSIITKKARGYLLFFQLLQIPLIALTN 479
Query: 179 HVEKKYGPRWGNIIVWSSLILGQPLCIMMYYHDF 212
K+ P GN+ W + +G P + Y F
Sbjct: 480 TKFKRRRPILGNVFFWFGICVG-PSVMCTLYITF 512
>gnl|CDD|217346 pfam03062, MBOAT, MBOAT, membrane-bound O-acyltransferase family.
The MBOAT (membrane bound O-acyl transferase) family of
membrane proteins contains a variety of acyltransferase
enzymes. A conserved histidine has been suggested to be
the active site residue.
Length = 309
Score = 35.9 bits (83), Expect = 0.012
Identities = 21/96 (21%), Positives = 32/96 (33%), Gaps = 10/96 (10%)
Query: 120 RHLYKPLVEQGYSRLT---ASSLVFFISAFMHE----YLVSVPLRTYKIWAFMGMMGQIP 172
R++YK L +L A+ F +SA H Y++ L +
Sbjct: 215 RYVYKRLGGSKNGKLNKFLATLATFLVSAVWHGLAWGYILWGLLHALFLILEKVFR---R 271
Query: 173 LSMLSRHVEKKYGPRWGNIIVWSSLILGQPLCIMMY 208
L P N+I W LG L ++Y
Sbjct: 272 LVRKIFLRSSGRRPLLLNVIFWLFAFLGGSLFFLLY 307
>gnl|CDD|220431 pfam09831, DUF2058, Uncharacterized protein conserved in bacteria
(DUF2058). This domain, found in various prokaryotic
proteins, has no known function.
Length = 177
Score = 33.3 bits (77), Expect = 0.048
Identities = 14/53 (26%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 24 ADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQE 76
D +K +A + K E +L Q A K IVA I+++ ++ I ++
Sbjct: 39 DDELKQAAEEA-KAEKAERDRELNRQRQAEAEQKAIVAQIKQLIEQNRIDRKD 90
>gnl|CDD|177725 PLN00110, PLN00110, flavonoid 3',5'-hydroxylase (F3'5'H);
Provisional.
Length = 504
Score = 33.7 bits (77), Expect = 0.068
Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 8/60 (13%)
Query: 134 LTASSLVFFISAFMHEYLVSVPLRTY----KIWAFMG---MMGQIPLSMLSRHVEKKYGP 186
L A++L+FFI+ F L+ P R + W +G ++G +P L++ + K+YGP
Sbjct: 7 LAAATLLFFITRFFIRSLLPKPSRKLPPGPRGWPLLGALPLLGNMPHVALAK-MAKRYGP 65
>gnl|CDD|236356 PRK08944, motB, flagellar motor protein MotB; Reviewed.
Length = 302
Score = 31.9 bits (73), Expect = 0.19
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 8/50 (16%)
Query: 24 ADIVKLHMAQASQEA---KKELQEQLEEQISEGA----SIKD-IVADIRE 65
+ VK A A ++ K+L +QLE++I +GA S+ I+ IRE
Sbjct: 130 SAEVKAEKAAAQEQIEDLVKKLAQQLEKEIEDGAIEIESLGQQIIIRIRE 179
>gnl|CDD|115617 pfam06972, DUF1296, Protein of unknown function (DUF1296). This
family represents a conserved region approximately 60
residues long within a number of plant proteins of
unknown function. Structural modelling suggests this
domain may bind nucleic acids.
Length = 60
Score = 29.4 bits (66), Expect = 0.25
Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 6/45 (13%)
Query: 54 ASIKDIVADIREIANKHCIPDQELIVL----NMDVVKATERLLKL 94
A ++ + I+E+ KH D ++ + NMD + ++LL
Sbjct: 3 AELRKTIQSIKEVVGKH--SDADIYAMLKECNMDPNETVQKLLSQ 45
>gnl|CDD|216134 pfam00816, Histone_HNS, H-NS histone family.
Length = 92
Score = 29.9 bits (68), Expect = 0.26
Identities = 11/55 (20%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 36 QEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLNMDVVKATER 90
+ ++L++++E A +A+IRE+A ++ + +EL+ +R
Sbjct: 4 EALIEKLEKEIEAA--RKAERAAALAEIRELAAEYGLTLEELLGGAAKKKAKKKR 56
>gnl|CDD|222874 PHA02557, 22, prohead core protein; Provisional.
Length = 271
Score = 31.2 bits (71), Expect = 0.30
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 12 EYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISE 52
E F TVFE VKL + ++ A+K +E +EE + E
Sbjct: 37 EKFSTVFEAAVKQHAVKLAESHIAEIAEK-AEELVEEALEE 76
>gnl|CDD|148491 pfam06898, YqfD, Putative stage IV sporulation protein YqfD. This
family consists of several putative bacterial stage IV
sporulation (SpoIV) proteins. YqfD of Bacillus subtilis
is known to be essential for efficient sporulation
although its exact function is unknown.
Length = 383
Score = 31.6 bits (72), Expect = 0.32
Identities = 20/79 (25%), Positives = 31/79 (39%), Gaps = 5/79 (6%)
Query: 2 EFVPPNKRSDEYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVA 61
K R + E VKL +A ++ KK +++LE++I + A IKD
Sbjct: 302 PLFLKWKLPISIVRETYYEVQDKV-VKLTKEEAVEKGKKLAKKKLEKEIDKDAKIKDEKV 360
Query: 62 DIREIANKHCIPDQELIVL 80
+ N L VL
Sbjct: 361 LHERVENGKV----RLRVL 375
>gnl|CDD|221429 pfam12118, SprA-related, SprA-related family. This protein is
found in bacteria. Proteins in this family are typically
between 234 to 465 amino acids in length. There is a
conserved GEV sequence motif.Most members are annotated
as being SprA-related.
Length = 261
Score = 30.9 bits (70), Expect = 0.48
Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 4/56 (7%)
Query: 32 AQASQ---EAKKEL-QEQLEEQISEGASIKDIVADIREIANKHCIPDQELIVLNMD 83
A+A+Q EA+ EL QE+ EE E + A+ + A + P + ++
Sbjct: 200 AEATQKENEARAELAQERQEEASEEDEAEALAGAENQITALEPLAPSTPQVDGQVE 255
>gnl|CDD|217679 pfam03701, UPF0181, Uncharacterized protein family (UPF0181).
This family contains small proteins of about 50 amino
acids of unknown function. The family includes YoaH.
Length = 52
Score = 28.4 bits (64), Expect = 0.52
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 23 LADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREIANK 69
L D+ L + QEA + +QE + + +S G +I + +IRE K
Sbjct: 2 LNDLPSLTHEE-QQEAVERIQELMAQGMSSGEAIAIVAQEIREKHQK 47
>gnl|CDD|213400 cd12193, B_zip1, basic leucine zipper DNA-binding and
multimerization region of GCN4 and related proteins.
Basic leucine zipper (bZIP) transcription factors act
in networks of homo- and hetero-dimers in the
regulation in a diverse set of cellular pathways.
Classical leucine zippers have alpha helices with
leucine residues 7 amino acids apart, which stabilize
dimerization with a parallel leucine zipper domain.
Dimerization creates a pair of basic regions that bind
DNA and undergo conformational change. GCN4 was
identified in Saccharomyces cerevisiae from mutations
in a deficiency in activation with the general amino
acid control pathway. GCN4 encodes a trans-activator of
amino acid biosynthetic genes containing 2 acidic
activation domains and a C-terminal bZIP domain,
comprised of a basic alpha-helical DNA-binding region
and a coiled-coil dimerization region.
Length = 54
Score = 28.4 bits (64), Expect = 0.54
Identities = 9/37 (24%), Positives = 20/37 (54%)
Query: 30 HMAQASQEAKKELQEQLEEQISEGASIKDIVADIREI 66
E K+L++++EE SE + ++D V +++
Sbjct: 16 RSRARKMERMKQLEDKVEELTSENSDLEDEVDRLKKA 52
>gnl|CDD|232867 TIGR00194, uvrC, excinuclease ABC, C subunit. This family consists
of the DNA repair enzyme UvrC, an ABC excinuclease
subunit which interacts with the UvrA/UvrB complex to
excise UV-damaged nucleotide segments [DNA metabolism,
DNA replication, recombination, and repair].
Length = 574
Score = 30.8 bits (70), Expect = 0.62
Identities = 17/55 (30%), Positives = 32/55 (58%), Gaps = 7/55 (12%)
Query: 36 QEAKKELQEQLEEQIS-----EGASIKDIVADIREIANKHCIPDQELIVLNMDVV 85
QE KEL++++E+ E A I+D +A +RE+ K + +LI ++D++
Sbjct: 193 QEVIKELEQKMEKASENLEFEEAARIRDQIAAVRELNEKQHVSLTDLI--DLDII 245
>gnl|CDD|222396 pfam13813, MBOAT_2, Membrane bound O-acyl transferase family.
Length = 83
Score = 28.8 bits (65), Expect = 0.73
Identities = 5/27 (18%), Positives = 9/27 (33%)
Query: 131 YSRLTASSLVFFISAFMHEYLVSVPLR 157
+R + F +S +H R
Sbjct: 46 LARYLRLLVAFLLSGLLHAAGDYAMGR 72
>gnl|CDD|236912 PRK11448, hsdR, type I restriction enzyme EcoKI subunit R;
Provisional.
Length = 1123
Score = 30.3 bits (69), Expect = 0.98
Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 5/64 (7%)
Query: 2 EFVPPNKRSDEYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVA 61
FVPP + E L ++L K + Q E Q E +++ + A
Sbjct: 133 PFVPPEDPENLLHALQQEVLTLKQQLELQ-----AREKAQSQALAEAQQQELVALEGLAA 187
Query: 62 DIRE 65
++ E
Sbjct: 188 ELEE 191
>gnl|CDD|216853 pfam02030, Lipoprotein_8, Hypothetical lipoprotein (MG045 family).
This family includes hypothetical lipoproteins, the
amino terminal part of this protein is related to
pfam01547, a family of solute binding proteins. This
suggests this family also has a solute binding function.
Length = 493
Score = 29.5 bits (66), Expect = 1.7
Identities = 24/119 (20%), Positives = 49/119 (41%), Gaps = 12/119 (10%)
Query: 1 MEFVPP-NKRSDEYFRTVFEEKGLADIVKLHMAQASQEAKKELQEQLEEQISE--GASIK 57
+ +V P SDE V + AD+ + ++ + K E+ I + ++K
Sbjct: 371 VNYVSPLKTISDENTGIVGKTGFEADLKRQKKQESFEIQTKYKTEKERNHIYDTYTKTLK 430
Query: 58 DIVADIREIANKHCIPDQELIVLNMDVVKATERLLKLSVSILHIHLV--PIPLLLISVL 114
++ + + + + + + +K +LKL +I I+L+ PI L S L
Sbjct: 431 FLL----NKNDSYELNNLNKKL--VSTIKKNYLILKLE-AIFWINLLEKPINPLQRSNL 482
>gnl|CDD|238559 cd01139, TroA_f, Periplasmic binding protein TroA_f. These
proteins are predicted to function as initial receptors
in the ABC metal ion uptake in eubacteria and archaea.
They belong to the TroA superfamily of helical backbone
metal receptor proteins that share a distinct fold and
ligand binding mechanism. A typical TroA protein is
comprised of two globular subdomains connected by a
single helix and can bind their ligands in the cleft
between these domains.
Length = 342
Score = 29.2 bits (66), Expect = 1.7
Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 8/61 (13%)
Query: 20 EKGLA---DIVKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQE 76
EK L D+V L++ + + + E+LE+ A I + D R+ K+ P
Sbjct: 85 EKVLTLKPDLVILNIWAKTTAEESGILEKLEQ-----AGIPVVFVDFRQKPLKNTTPSMR 139
Query: 77 L 77
L
Sbjct: 140 L 140
>gnl|CDD|225682 COG3140, COG3140, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 60
Score = 27.1 bits (60), Expect = 1.7
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 36 QEAKKELQEQLEEQISEGASIKDIVADIREI 66
Q+A + +QE + E +S G +I + ++RE
Sbjct: 14 QKAVERIQELMAEGMSSGEAIALVAQELREN 44
>gnl|CDD|237177 PRK12704, PRK12704, phosphodiesterase; Provisional.
Length = 520
Score = 29.4 bits (67), Expect = 1.8
Identities = 14/37 (37%), Positives = 25/37 (67%), Gaps = 2/37 (5%)
Query: 35 SQEAKKELQEQLEEQISEGAS--IKDIVADIREIANK 69
++EAK+ L E++EE+ A+ IK+I + +E A+K
Sbjct: 152 AEEAKEILLEKVEEEARHEAAVLIKEIEEEAKEEADK 188
>gnl|CDD|218753 pfam05794, Tcp11, T-complex protein 11. This family consists of
several eukaryotic T-complex protein 11 (Tcp11) related
sequences. Tcp11 is only expressed in fertile adult
mammalian testes and is thought to be important in sperm
function and fertility. The family also contains the
yeast Sok1 protein which is known to suppress cyclic
AMP-dependent protein kinase mutants.
Length = 431
Score = 29.2 bits (66), Expect = 1.9
Identities = 24/80 (30%), Positives = 39/80 (48%), Gaps = 13/80 (16%)
Query: 20 EKGLADIVKLH------MAQASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIP 73
E G DIVKL + + A+ E ++L+E+ISE S+ DIV +R I
Sbjct: 93 EHGALDIVKLAKFIINILKKLCAPARDEEVKKLKEKISESQSVDDIVEGLRGIF------ 146
Query: 74 DQELIVLNMDVVKATERLLK 93
+ L ++ +D+ R L+
Sbjct: 147 -EVLELMKLDMANFQIRSLR 165
>gnl|CDD|236081 PRK07735, PRK07735, NADH dehydrogenase subunit C; Validated.
Length = 430
Score = 28.8 bits (64), Expect = 2.4
Identities = 12/34 (35%), Positives = 19/34 (55%)
Query: 19 EEKGLADIVKLHMAQASQEAKKELQEQLEEQISE 52
EK L D+ K +A +EA+K L + +IS+
Sbjct: 3 PEKDLEDLKKEAARRAKEEARKRLVAKHGAEISK 36
>gnl|CDD|223910 COG0840, Tar, Methyl-accepting chemotaxis protein [Cell motility
and secretion / Signal transduction mechanisms].
Length = 408
Score = 28.8 bits (64), Expect = 2.6
Identities = 10/38 (26%), Positives = 18/38 (47%)
Query: 30 HMAQASQEAKKELQEQLEEQISEGASIKDIVADIREIA 67
+ QE +EL E +++ I++I + I IA
Sbjct: 212 QAVEQMQEIAEELAEVVKKLSESSQEIEEITSVINSIA 249
>gnl|CDD|222447 pfam13904, DUF4207, Domain of unknown function (DUF4207). This
family is found in eukaryotes; it has several conserved
tryptophan residues. The function is not known.
Length = 261
Score = 28.5 bits (64), Expect = 2.7
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 9/56 (16%)
Query: 5 PPNKRSDEYFRTVFEEKGLADIVKLHMAQASQEAK--KELQEQLEE----QISEGA 54
P S E + +E ++ KL Q +E + K+ ++Q EE Q +E A
Sbjct: 171 PERNVSQEEAKKRLQE---WELKKLKQQQQKREEERRKQRKKQQEEEERKQKAEEA 223
>gnl|CDD|217115 pfam02575, YbaB_DNA_bd, YbaB/EbfC DNA-binding family. This is a
family of DNA-binding proteins. Members of this family
form homodimers which bind DNA via a tweezer-like
structure. The conformation of the DNA is changed when
bound to these proteins. In bacteria, these proteins
may play a role in DNA replication-recovery following
DNA damage.
Length = 92
Score = 27.1 bits (61), Expect = 3.1
Identities = 10/25 (40%), Positives = 14/25 (56%)
Query: 31 MAQASQEAKKELQEQLEEQISEGAS 55
AQ QE ++ QE+L + EG S
Sbjct: 3 QAQQMQEKMEKAQEELANKEVEGTS 27
>gnl|CDD|179941 PRK05114, PRK05114, hypothetical protein; Provisional.
Length = 59
Score = 26.1 bits (58), Expect = 3.2
Identities = 8/30 (26%), Positives = 18/30 (60%)
Query: 36 QEAKKELQEQLEEQISEGASIKDIVADIRE 65
Q+A + +QE + + +S G +I + ++R
Sbjct: 14 QKAVERIQELMAQGMSSGEAIALVAEELRA 43
>gnl|CDD|177847 PLN02196, PLN02196, abscisic acid 8'-hydroxylase.
Length = 463
Score = 28.4 bits (63), Expect = 3.5
Identities = 19/80 (23%), Positives = 33/80 (41%), Gaps = 5/80 (6%)
Query: 97 SILHIHLVPIPLLLISV-----LCIISCRHLYKPLVEQGYSRLTASSLVFFISAFMHEYL 151
S+ H++ P ++IS +++ HL+KP R+ +FF H L
Sbjct: 70 SVFKTHVLGCPCVMISSPEAAKFVLVTKSHLFKPTFPASKERMLGKQAIFFHQGDYHAKL 129
Query: 152 VSVPLRTYKIWAFMGMMGQI 171
+ LR + A M+ I
Sbjct: 130 RKLVLRAFMPDAIRNMVPDI 149
>gnl|CDD|184771 PRK14623, PRK14623, hypothetical protein; Provisional.
Length = 106
Score = 27.1 bits (60), Expect = 3.8
Identities = 22/73 (30%), Positives = 33/73 (45%), Gaps = 11/73 (15%)
Query: 28 KLHMAQASQEAKKE------LQEQ-----LEEQISEGASIKDIVADIREIANKHCIPDQE 76
KL AQ EA K+ + EQ L+ ++ IK I D + +K + D
Sbjct: 9 KLKEAQQKVEATKKRLDTVLIDEQSSDGLLKVTVTANREIKSISIDDELLEDKEQLEDYL 68
Query: 77 LIVLNMDVVKATE 89
++ LN + KATE
Sbjct: 69 VLTLNKAIEKATE 81
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 28.2 bits (63), Expect = 4.3
Identities = 9/40 (22%), Positives = 20/40 (50%)
Query: 31 MAQASQEAKKELQEQLEEQISEGASIKDIVADIREIANKH 70
+ + E K+L+E ++E E A + + +I+E +
Sbjct: 376 ELEKALERLKQLEEAIQELKEELAELSAALEEIQEELEEL 415
>gnl|CDD|143418 cd07100, ALDH_SSADH1_GabD1, Mycobacterium tuberculosis
succinate-semialdehyde dehydrogenase 1-like.
Succinate-semialdehyde dehydrogenase 1 (SSADH1, GabD1,
EC=1.2.1.16) catalyzes the NADP(+)-dependent oxidation
of succinate semialdehyde (SSA) to succinate. SSADH
activity in Mycobacterium tuberculosis (Mtb) is encoded
by both gabD1 (Rv0234c) and gabD2 (Rv1731). The Mtb
GabD1 SSADH1 reportedly is an enzyme of the
gamma-aminobutyrate shunt, which forms a functional link
between two TCA half-cycles by converting
alpha-ketoglutarate to succinate.
Length = 429
Score = 27.8 bits (63), Expect = 4.6
Identities = 9/23 (39%), Positives = 17/23 (73%)
Query: 34 ASQEAKKELQEQLEEQISEGASI 56
A ++ + EL EQ+EE ++ GA++
Sbjct: 281 ARKDLRDELHEQVEEAVAAGATL 303
>gnl|CDD|168717 PRK06882, PRK06882, acetolactate synthase 3 catalytic subunit;
Validated.
Length = 574
Score = 28.0 bits (62), Expect = 4.8
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 23 LADIVKLHMAQASQEAKKELQEQLEEQISEGASIKD--IVADIREIANKHCIPDQ 75
L D KL A + + ++LEE++++ SIKD + D+ +H P Q
Sbjct: 501 LPDFAKLAEAYGHVGIQIDTPDELEEKLTQAFSIKDKLVFVDVNVDETEHVYPMQ 555
>gnl|CDD|239936 cd04490, PolII_SU_OBF, PolII_SU_OBF: A subfamily of OB folds
corresponding to the OB fold found in Pyrococcus abyssi
DNA polymerase II (PolII) small subunit. PolII is a
family D DNA polymerase, having a 3-prime to 5-prime
exonuclease activity. P. abyssi PolII is heterodimeric.
The large subunit appears to be the polymerase, and the
small subunit may be the exonuclease. The small subunit
contains a calcineurin-like phosphatase superfamily
domain C-terminal to this OB-fold domain.
Length = 79
Score = 26.1 bits (58), Expect = 5.5
Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 9/52 (17%)
Query: 54 ASIKDIVADIREIANKHCI-----PDQELIVL----NMDVVKATERLLKLSV 96
SI +V D+R N H I + VL ++ + E +L V
Sbjct: 2 VSIIGMVNDVRSTKNGHRIVELEDTTGRITVLLTKDKEELFEEAEDILPDEV 53
>gnl|CDD|180814 PRK07057, sdhA, succinate dehydrogenase flavoprotein subunit;
Reviewed.
Length = 591
Score = 27.9 bits (62), Expect = 5.9
Identities = 16/58 (27%), Positives = 28/58 (48%), Gaps = 8/58 (13%)
Query: 48 EQISEGASIKDIVADIREIANKHC--IPDQELIVLNMDVVKATERLLKLSVSILHIHL 103
++ + G +D+ DIR KH Q L +D + E++L L+ + +IHL
Sbjct: 451 DKSTSGEYAQDVANDIRATMQKHAGVFRTQAL----LD--EGVEQILALAERVENIHL 502
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 27.5 bits (62), Expect = 6.3
Identities = 11/42 (26%), Positives = 22/42 (52%), Gaps = 5/42 (11%)
Query: 35 SQEAKKELQEQLEEQISEGASIKDIVADIREIANK-----HC 71
++E +E E+LE G+ D++ ++++ A K HC
Sbjct: 110 TEEEIEEYLEKLERLKEWGSLADDLIKEVKKEAAKRMVCPHC 151
>gnl|CDD|131117 TIGR02062, RNase_B, exoribonuclease II. This family consists of
exoribonuclease II, the product of the rnb gene, as
found in a number of gamma proteobacteria. In
Escherichia coli, it is one of eight different
exoribonucleases. It is involved in mRNA degradation and
tRNA precursor end processing [Transcription,
Degradation of RNA].
Length = 639
Score = 27.5 bits (61), Expect = 6.5
Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 49 QISEGASIKDIVADIREIANKHCIPDQELIVLNM 82
+SE + DIVA+ R IAN+ I ++ +I+ N+
Sbjct: 364 ILSEKGEVLDIVAEPRRIANR--IVEEAMIIANI 395
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 27.7 bits (62), Expect = 6.7
Identities = 13/47 (27%), Positives = 23/47 (48%), Gaps = 2/47 (4%)
Query: 8 KRSDEYFRTVFEEKG-LADIVK-LHMAQASQEAKKELQEQLEEQISE 52
R DE + + + + +I K + + +E KE E+LEE +S
Sbjct: 702 NRLDELSQELSDASRKIGEIEKEIEQLEQEEEKLKERLEELEEDLSS 748
>gnl|CDD|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E'
[Transcription].
Length = 183
Score = 26.9 bits (60), Expect = 7.2
Identities = 14/61 (22%), Positives = 32/61 (52%), Gaps = 6/61 (9%)
Query: 18 FEEKGLADIVKLHMAQASQEAKKELQEQLEEQISEGASIKDI-----VADIREIANKHCI 72
++ L D V++ + ++ ++ ++E+L+E+ EG D+ V D++EI +
Sbjct: 2 YKLVELEDTVRIPPSYFGEDLEEAVKEELKEKY-EGKLDGDVGLVVLVLDVKEIGEGIIV 60
Query: 73 P 73
P
Sbjct: 61 P 61
>gnl|CDD|146751 pfam04279, IspA, Intracellular septation protein A.
Length = 176
Score = 26.7 bits (60), Expect = 7.4
Identities = 16/68 (23%), Positives = 33/68 (48%), Gaps = 12/68 (17%)
Query: 125 PLVEQGYSRLTASSLVFFI-SAFMHEYLV-SVPLRT---YKIWAFMGMM-----GQIPLS 174
L ++G+ +L +FF+ A ++EY+ + T +K++ MG+ Q P
Sbjct: 110 ELPDEGWRKLNLRWALFFLFMAVLNEYVAFNFSTDTWVNFKVFGLMGLTLVFTLAQGP-- 167
Query: 175 MLSRHVEK 182
L +H+ +
Sbjct: 168 YLYKHLLE 175
>gnl|CDD|225349 COG2739, COG2739, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 105
Score = 26.2 bits (58), Expect = 7.5
Identities = 10/39 (25%), Positives = 25/39 (64%), Gaps = 1/39 (2%)
Query: 28 KLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIREI 66
KL + + + +KEL ++L+E I++ +++I+ D+ +
Sbjct: 67 KLKLYE-KYKIRKELYDKLKELITDPEELREILEDLDNL 104
>gnl|CDD|236854 PRK11125, nrfA, cytochrome c nitrite reductase subunit c552;
Provisional.
Length = 480
Score = 27.3 bits (61), Expect = 8.0
Identities = 28/121 (23%), Positives = 51/121 (42%), Gaps = 35/121 (28%)
Query: 20 EKGLADIVKLHMAQASQEAKKELQEQLEEQISE-----------GAS---IKDIVADIRE 65
++ L +V + +L+ + E+Q+ + GA+ +K I+ DIR
Sbjct: 323 KEALQKVVAER-----KAKVNDLKIKAEDQLVKAHFEAKAAWDAGATEAEMKPILTDIRH 377
Query: 66 --------IANKHCI----PDQELIVLNMDVVKATERLLKLSVSILHIHLV--PIPLLLI 111
IA+ H I P++ L +L + KA + KL+ +L + PI + I
Sbjct: 378 AQWRWDYAIAS-HGIHMHAPEEALRILGTALDKAADARTKLAR-LLAKKGITDPIQIPDI 435
Query: 112 S 112
S
Sbjct: 436 S 436
>gnl|CDD|235026 PRK02292, PRK02292, V-type ATP synthase subunit E; Provisional.
Length = 188
Score = 26.9 bits (60), Expect = 8.1
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 2/39 (5%)
Query: 27 VKLHMAQASQEAKKELQEQLEEQISEGASIKDIVADIRE 65
KL + A+KE+ E + Q+ + I + D RE
Sbjct: 66 AKLEAKRERLNARKEVLEDVRNQVED--EIASLDGDKRE 102
>gnl|CDD|133397 cd04769, HTH_MerR2, Helix-Turn-Helix DNA binding domain of
MerR2-like transcription regulators. Helix-turn-helix
(HTH) transcription regulator MerR2 and related
proteins. MerR2 in Bacillus cereus RC607 regulates
resistance to organomercurials. The MerR family
transcription regulators have been shown to mediate
responses to stress including exposure to heavy metals,
drugs, or oxygen radicals in eubacterial and some
archaeal species. They regulate transcription by
reconfiguring the spacer between the -35 and -10
promoter elements. A typical MerR regulator is comprised
of two distinct domains that harbor the regulatory
(effector-binding) site and the active (DNA-binding)
site. Their N-terminal domains are homologous and
contain a DNA-binding winged HTH motif, while the
C-terminal domains are often dissimilar and bind
specific coactivator molecules such as metal ions,
drugs, and organic substrates.
Length = 116
Score = 26.2 bits (58), Expect = 8.8
Identities = 9/36 (25%), Positives = 20/36 (55%)
Query: 30 HMAQASQEAKKELQEQLEEQISEGASIKDIVADIRE 65
H+ QA ++ K+E++ Q+ E A + A +++
Sbjct: 79 HLQQALEDKKQEIRAQITELQQLLARLDAFEASLKD 114
>gnl|CDD|236408 PRK09200, PRK09200, preprotein translocase subunit SecA;
Reviewed.
Length = 790
Score = 27.2 bits (61), Expect = 8.9
Identities = 16/57 (28%), Positives = 30/57 (52%), Gaps = 12/57 (21%)
Query: 20 EKGLADIVKL--HMAQASQEAKKELQEQ---LEEQISEGASIKDIVAD----IREIA 67
K + I KL M+ S E EL+++ +E+++ G ++ DI+ + +RE A
Sbjct: 18 RKIVKQINKLEGKMSSLSDE---ELRQKTIEFKERLASGKTLDDILPEAFAVVREAA 71
>gnl|CDD|218769 pfam05833, FbpA, Fibronectin-binding protein A N-terminus (FbpA).
This family consists of the N-terminal region of the
prokaryotic fibronectin-binding protein. Fibronectin
binding is considered to be an important virulence
factor in streptococcal infections. Fibronectin is a
dimeric glycoprotein that is present in a soluble form
in plasma and extracellular fluids; it is also present
in a fibrillar form on cell surfaces. Both the soluble
and cellular forms of fibronectin may be incorporated
into the extracellular tissue matrix. While fibronectin
has critical roles in eukaryotic cellular processes,
such as adhesion, migration and differentiation, it is
also a substrate for the attachment of bacteria. The
binding of pathogenic Streptococcus pyogenes and
Staphylococcus aureus to epithelial cells via
fibronectin facilitates their internalisation and
systemic spread within the host.
Length = 447
Score = 26.8 bits (60), Expect = 9.8
Identities = 11/32 (34%), Positives = 21/32 (65%), Gaps = 3/32 (9%)
Query: 36 QEAKKELQ--EQLEEQISEGASIKDIVADIRE 65
+E K+E++ E +E Q+ S++D+ +IRE
Sbjct: 396 EETKEEIEYLESVEAQLENAESLEDL-EEIRE 426
>gnl|CDD|182731 PRK10788, PRK10788, periplasmic folding chaperone; Provisional.
Length = 623
Score = 26.9 bits (60), Expect = 9.8
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 1/47 (2%)
Query: 33 QASQEAKKELQEQLEEQISEGASIKDIVADIREIANKHCIPDQELIV 79
QA Q + LQ+QL +Q SE A+ + + +R+ I D+ L+
Sbjct: 57 QAFQSERNRLQQQLGDQFSELAANEGYMKQLRQQVLNRLI-DEALLD 102
>gnl|CDD|224496 COG1580, FliL, Flagellar basal body-associated protein [Cell
motility and secretion].
Length = 159
Score = 26.5 bits (59), Expect = 9.8
Identities = 7/31 (22%), Positives = 18/31 (58%)
Query: 29 LHMAQASQEAKKELQEQLEEQISEGASIKDI 59
L + ++ K E+++++ + EG +KD+
Sbjct: 121 LSTPEGKEKLKAEIKDRINTILKEGQVVKDV 151
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
0.325 0.139 0.415
Gapped
Lambda K H
0.267 0.0675 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,836,624
Number of extensions: 1138745
Number of successful extensions: 2400
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2389
Number of HSP's successfully gapped: 105
Length of query: 228
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 134
Effective length of database: 6,768,326
Effective search space: 906955684
Effective search space used: 906955684
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 57 (25.8 bits)