RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8149
(182 letters)
>gnl|CDD|197842 smart00717, SANT, SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding
domains.
Length = 49
Score = 37.6 bits (88), Expect = 2e-04
Identities = 16/49 (32%), Positives = 25/49 (51%), Gaps = 4/49 (8%)
Query: 31 GNKWTAEDIEMLKETVRKFG-DELVIISDRIKDRTISQIKS---NLKKK 75
+WT E+ E+L E V+K+G + I+ + RT Q + NL K
Sbjct: 1 KGEWTEEEDELLIELVKKYGKNNWEKIAKELPGRTAEQCRERWRNLLKP 49
>gnl|CDD|215818 pfam00249, Myb_DNA-binding, Myb-like DNA-binding domain. This
family contains the DNA binding domains from Myb
proteins, as well as the SANT domain family.
Length = 47
Score = 35.2 bits (82), Expect = 0.001
Identities = 14/40 (35%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 32 NKWTAEDIEMLKETVRKFG-DELVIISDRIKDRTISQIKS 70
WT E+ E+L E V+K G I+ + RT +Q K+
Sbjct: 2 GPWTPEEDELLIEAVKKHGNGNWSKIAKHLPGRTDNQCKN 41
>gnl|CDD|238096 cd00167, SANT, 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding
domains. Tandem copies of the domain bind telomeric DNA
tandem repeatsas part of the capping complex. Binding
is sequence dependent for repeats which contain the G/C
rich motif [C2-3 A (CA)1-6]. The domain is also found
in regulatory transcriptional repressor complexes where
it also binds DNA.
Length = 45
Score = 34.5 bits (80), Expect = 0.002
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 33 KWTAEDIEMLKETVRKFGDE-LVIISDRIKDRTISQIKS 70
WT E+ E+L E V+K+G I+ + RT Q +
Sbjct: 1 PWTEEEDELLLEAVKKYGKNNWEKIAKELPGRTPKQCRE 39
>gnl|CDD|215119 PLN02187, PLN02187, rooty/superroot1.
Length = 462
Score = 37.0 bits (85), Expect = 0.003
Identities = 16/40 (40%), Positives = 28/40 (70%), Gaps = 2/40 (5%)
Query: 26 PDSPSGNKWTAEDIEMLKETVRKFGDELVIISDRIKDRTI 65
P++P GN ++ + ++ + ET RK G +++ISD + DRTI
Sbjct: 213 PNNPCGNVYSHDHLKKVAETARKLG--IMVISDEVYDRTI 250
>gnl|CDD|206092 pfam13921, Myb_DNA-bind_6, Myb-like DNA-binding domain. This
family contains the DNA binding domains from Myb
proteins, as well as the SANT domain family.
Length = 59
Score = 32.3 bits (74), Expect = 0.017
Identities = 14/59 (23%), Positives = 27/59 (45%), Gaps = 10/59 (16%)
Query: 34 WTAEDIEMLKETVRKFGDELVIISD-------RIKDRTISQIKSNLKKKAF---EDAGL 82
WT E+ E L + V K+G++ I++ +DR +++ + + ED L
Sbjct: 1 WTEEEDEKLLKLVEKYGNDWKQIAEELGRTPSACRDRWRRKLRPKRSRGPWTKEEDQRL 59
>gnl|CDD|181036 PRK07568, PRK07568, aspartate aminotransferase; Provisional.
Length = 397
Score = 34.8 bits (81), Expect = 0.017
Identities = 15/35 (42%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 24 STPDSPSGNKWTAEDIEMLKETVRKFGDELVIISD 58
S P +P+G +T E++EML E +K L +ISD
Sbjct: 169 SNPGNPTGVVYTKEELEMLAEIAKKHD--LFLISD 201
>gnl|CDD|212556 cd11658, SANT_DMAP1_like, SANT/myb-like domain of Human Dna
Methyltransferase 1 Associated Protein 1-like. These
proteins are members of the SANT/myb group. SANT is
named after 'SWI3, ADA2, N-CoR and TFIIIB', several
factors that share this domain. The SANT domain
resembles the 3 alpha-helix bundle of the DNA-binding
Myb domains and is found in a diverse set of proteins.
Length = 46
Score = 31.2 bits (71), Expect = 0.032
Identities = 14/45 (31%), Positives = 24/45 (53%), Gaps = 7/45 (15%)
Query: 34 WTAEDIEMLKETVRKFGDELVIISDRI---KDRTISQIKSNLKKK 75
WT E+ + L + V++F +I DR K R++ +LK+K
Sbjct: 1 WTKEETDYLFDLVKRFDLRWNVILDRYPFQKGRSV----EDLKEK 41
>gnl|CDD|224090 COG1168, MalY, Bifunctional PLP-dependent enzyme with
beta-cystathionase and maltose regulon repressor
activities [Amino acid transport and metabolism].
Length = 388
Score = 33.8 bits (78), Expect = 0.038
Identities = 12/35 (34%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 26 PDSPSGNKWTAEDIEMLKETVRKFGDELVIISDRI 60
P +P+G WT E++ + E + G + +ISD I
Sbjct: 167 PHNPTGRVWTKEELRKIAELCLRHG--VRVISDEI 199
>gnl|CDD|212558 cd11660, SANT_TRF, Telomere repeat binding factor-like
DNA-binding domains of the SANT/myb-like family. Human
telomere repeat binding factors, TRF1 and TRF2,
function as part of the 6 component shelterin complex.
TRF2 binds DNA and recruits RAP1 (via binding to the
RAP1 protein c-terminal (RCT)) and TIN2 in the
protection of telomeres from DNA repair machinery.
Metazoan shelterin consists of 3 DNA binding proteins
(TRF2, TRF1, and POT1) and 3 recruited proteins that
bind to one or more of these DNA-binding proteins
(RAP1, TIN2, TPP1). Schizosaccharomyces pombe TAZ1 is
an orthlog and binds RAP1. Human TRF1 and TRF2 bind
double-stranded DNA. hTRF2 consists of a basic
N-terminus, a TRF homology domain, the RAP1 binding
motif (RBM), the TIN2 binding motif (TBM) and a
myb-like DNA binding domain, SANT, named after 'SWI3,
ADA2, N-CoR and TFIIIB', several factors that share
this domain. Tandem copies of the domain bind telomeric
DNA tandem repeats as part of the capping complex. The
single myb-like domain of TRF-type proteins is similar
to the tandem myb_like domains found in yeast RAP1.
Length = 50
Score = 31.0 bits (71), Expect = 0.039
Identities = 17/49 (34%), Positives = 25/49 (51%), Gaps = 7/49 (14%)
Query: 33 KWTAEDIEMLKETVRKFGD----ELVIISDRIKDRTISQIK---SNLKK 74
KWT E+ E L E V K+G +++ + +RT +K NLKK
Sbjct: 2 KWTDEEDEALVEGVEKYGVGNWAKILKDYFFVNNRTSVDLKDKWRNLKK 50
>gnl|CDD|224231 COG1312, UxuA, D-mannonate dehydratase [Carbohydrate transport
and metabolism].
Length = 362
Score = 33.1 bits (76), Expect = 0.064
Identities = 15/59 (25%), Positives = 22/59 (37%), Gaps = 11/59 (18%)
Query: 26 PDSPSGNKWTAEDIEMLKETVRKFGDEL-----VIISDRIK------DRTISQIKSNLK 73
P+G W E+I KE + G V + + IK DR I K ++
Sbjct: 32 HHIPAGEVWPVEEILKRKEEIESAGLTWSVVESVPVHEDIKLGTPTRDRYIENYKQTIR 90
>gnl|CDD|237191 PRK12757, PRK12757, cell division protein FtsN; Provisional.
Length = 256
Score = 32.3 bits (74), Expect = 0.100
Identities = 16/54 (29%), Positives = 19/54 (35%), Gaps = 3/54 (5%)
Query: 85 QQQVAPPQQIVQ---QVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQ 135
+Q P+ VQ Q QQQ PQ V P + P PV Q
Sbjct: 109 EQTPQVPRSTVQIQQQAQQQQPPATTAQPQPVTPPRQTTAPVQPQTPAPVRTQP 162
Score = 31.9 bits (73), Expect = 0.12
Identities = 14/52 (26%), Positives = 16/52 (30%)
Query: 85 QQQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQQ 136
+ V QQ QQ Q QT V QT A V +A
Sbjct: 116 RSTVQIQQQAQQQQPPATTAQPQPVTPPRQTTAPVQPQTPAPVRTQPAAPVT 167
Score = 30.4 bits (69), Expect = 0.45
Identities = 15/49 (30%), Positives = 16/49 (32%)
Query: 85 QQQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSA 133
Q Q P Q + AP QTP V Q A V V A
Sbjct: 124 QAQQQQPPATTAQPQPVTPPRQTTAPVQPQTPAPVRTQPAAPVTQAVEA 172
Score = 28.9 bits (65), Expect = 1.2
Identities = 13/52 (25%), Positives = 16/52 (30%)
Query: 84 IQQQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQ 135
IQQQ Q Q Q VQ T +T PV + +
Sbjct: 121 IQQQAQQQQPPATTAQPQPVTPPRQTTAPVQPQTPAPVRTQPAAPVTQAVEA 172
Score = 28.1 bits (63), Expect = 2.4
Identities = 15/58 (25%), Positives = 20/58 (34%), Gaps = 1/58 (1%)
Query: 91 PQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQQLLSGSHKSAEVT 148
Q+ + VQ Q Q Q P + V T PV Q + +A VT
Sbjct: 111 TPQVPRSTVQIQQQAQQQQPPATTAQPQPVTPPRQTTA-PVQPQTPAPVRTQPAAPVT 167
>gnl|CDD|181642 PRK09082, PRK09082, methionine aminotransferase; Validated.
Length = 386
Score = 32.6 bits (75), Expect = 0.10
Identities = 12/34 (35%), Positives = 21/34 (61%), Gaps = 2/34 (5%)
Query: 25 TPDSPSGNKWTAEDIEMLKETVRKFGDELVIISD 58
TP +PSG W+A D+ L + + G ++ ++SD
Sbjct: 171 TPHNPSGTVWSAADMRALWQLIA--GTDIYVLSD 202
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 31.9 bits (73), Expect = 0.20
Identities = 17/106 (16%), Positives = 38/106 (35%), Gaps = 3/106 (2%)
Query: 76 AFEDAGLPIQQQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQ 135
+ + + +V+ V + + VV A + V + PV+ Q
Sbjct: 869 VVAEVPVAAAVEPVVSAPVVEAVAEVVEEPVVVAEPQPEEVVVVETTHPEVIAAPVTEQP 928
Query: 136 QLLSGSHKSAEVTLNMLNAHPESEVDVEGLPEEVKLQFDTTAQQVA 181
Q+++ +S + H E V+ + +++ +T VA
Sbjct: 929 QVIT---ESDVAVAQEVAEHAEPVVEPQDETADIEEAAETAEVVVA 971
Score = 28.9 bits (65), Expect = 1.7
Identities = 12/42 (28%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 88 VAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPV 129
V PQ VQ Q++ ++V P + + P + V + PV
Sbjct: 847 VVRPQD-VQVEEQREAEEVQVQPVVAEVPVAAAVEPVVSAPV 887
>gnl|CDD|226870 COG4464, CapC, Capsular polysaccharide biosynthesis protein
[Carbohydrate transport and metabolism / Cell envelope
biogenesis, outer membrane].
Length = 254
Score = 31.2 bits (71), Expect = 0.21
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 7/77 (9%)
Query: 23 HSTPDSPSGNKWTAEDIEMLKETVRKFGDELVIISDRIKDR---TISQIKSNLKK--KAF 77
H PD G K E + ML+E VR+ ++V S + R I ++K + +
Sbjct: 7 HILPDIDDGPKSLEESLAMLREAVRQGVTKIVATSHHLHGRYENPIEKVKEKANQLNEIL 66
Query: 78 EDAGLPIQQQVAPPQQI 94
+ + + +V P Q+I
Sbjct: 67 KKEAIDL--KVLPGQEI 81
>gnl|CDD|213963 TIGR04350, C_S_lyase_PatB, putative C-S lyase. Members of this
subfamily are probable C-S lyases from a family of
pyridoxal phosphate-dependent enzymes that tend to be
(mis)annotated as probable aminotransferases. One member
is PatB of Bacillus subtilis, a proven C-S-lyase.
Another is the virulence factor cystalysin from
Treponema denticola, whose hemolysin activity may stem
from H2S production. Members of the seed alignment occur
next to examples of the enzyme 5-histidylcysteine
sulfoxide synthase, from ovothiol A biosynthesis, and
would be expected to perform a C-S cleavage of
5-histidylcysteine sulfoxide to leave
1-methyl-4-mercaptohistidine (ovothiol A).
Length = 384
Score = 31.1 bits (71), Expect = 0.25
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 26 PDSPSGNKWTAEDIEMLKETVRKFGDELVIISDRI 60
P +P G WT E++ L E + +V++SD I
Sbjct: 166 PHNPVGRVWTREELTRLAELCLRHN--VVVVSDEI 198
>gnl|CDD|215074 PLN00145, PLN00145, tyrosine/nicotianamine aminotransferase;
Provisional.
Length = 430
Score = 31.3 bits (71), Expect = 0.26
Identities = 12/37 (32%), Positives = 24/37 (64%), Gaps = 2/37 (5%)
Query: 26 PDSPSGNKWTAEDIEMLKETVRKFGDELVIISDRIKD 62
P++P G+ ++ E + + ET RK G +++I+D + D
Sbjct: 199 PNNPCGSVYSYEHLAKIAETARKLG--ILVIADEVYD 233
>gnl|CDD|236300 PRK08576, PRK08576, hypothetical protein; Provisional.
Length = 438
Score = 31.2 bits (71), Expect = 0.28
Identities = 12/44 (27%), Positives = 23/44 (52%), Gaps = 1/44 (2%)
Query: 17 DLTLQLHSTPDSPSGNKW-TAEDIEMLKETVRKFGDELVIISDR 59
D+ + + N+W T +E L+E +R+ D L+++ DR
Sbjct: 296 DVPMPIEKYGMPTHSNRWCTKLKVEALEEAIRELEDGLLVVGDR 339
>gnl|CDD|216477 pfam01397, Terpene_synth, Terpene synthase, N-terminal domain.
It has been suggested that this gene family be
designated tps (for terpene synthase). It has been
split into six subgroups on the basis of phylogeny,
called tpsa-tpsf. tpsa includes vetispiridiene
synthase, 5-epi- aristolochene synthase, and
(+)-delta-cadinene synthase. tpsb includes (-)-limonene
synthase. tpsc includes kaurene synthase A. tpsd
includes taxadiene synthase, pinene synthase, and
myrcene synthase. tpse includes kaurene synthase B.
tpsf includes linalool synthase.
Length = 177
Score = 30.2 bits (69), Expect = 0.37
Identities = 11/27 (40%), Positives = 15/27 (55%)
Query: 22 LHSTPDSPSGNKWTAEDIEMLKETVRK 48
L T D + ++ E +E LKE VRK
Sbjct: 6 LSYTADMQTEDEKCLERLESLKEEVRK 32
>gnl|CDD|215193 PLN02337, PLN02337, lipoxygenase.
Length = 866
Score = 30.8 bits (70), Expect = 0.38
Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 12/51 (23%)
Query: 20 LQLHSTP-------DSPSGNKWTAEDIEMLKETVRKFGDELVIISDRIKDR 63
L HS+ D+P +WT+ D E L E ++FG+ LV I +RI D
Sbjct: 777 LSRHSSDEVYLGQRDTP---EWTS-DAEPL-EAFKRFGERLVEIENRIVDM 822
>gnl|CDD|235172 PRK03906, PRK03906, mannonate dehydratase; Provisional.
Length = 385
Score = 30.2 bits (69), Expect = 0.54
Identities = 15/48 (31%), Positives = 20/48 (41%), Gaps = 8/48 (16%)
Query: 22 LHSTPDSPSGNKWTAEDIEMLKETVRKFGDEL-VI----ISDRIKDRT 64
LH D P G W E+I K + G E V+ + + IK T
Sbjct: 31 LH---DIPVGEVWPVEEILARKAEIEAAGLEWSVVESVPVHEDIKTGT 75
>gnl|CDD|235124 PRK03427, PRK03427, cell division protein ZipA; Provisional.
Length = 333
Score = 30.0 bits (68), Expect = 0.58
Identities = 16/52 (30%), Positives = 19/52 (36%)
Query: 85 QQQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQQ 136
Q P QQ V V Q V APQ Q + + A P PV+
Sbjct: 136 PQPEQPLQQPVSPQVAPAPQPVHSAPQPAQQAFQPAEPVAAPQPEPVAEPAP 187
Score = 28.8 bits (65), Expect = 1.5
Identities = 29/91 (31%), Positives = 36/91 (39%), Gaps = 10/91 (10%)
Query: 83 PIQQQVAP-PQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQQLLSGS 141
+ Q AP P Q Q VQQ Q Q Q +Q P V VA P PV + Q +
Sbjct: 112 QVPPQHAPRPAQPAPQPVQQPAYQP-QPEQPLQQP---VSPQVAPAPQPVHSAPQPAQQA 167
Query: 142 HKSAEVTLNMLNAHPESEVDVEGLPEEVKLQ 172
+ AE A P+ E E P K +
Sbjct: 168 FQPAE-----PVAAPQPEPVAEPAPVMDKPK 193
>gnl|CDD|237863 PRK14949, PRK14949, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 944
Score = 30.1 bits (68), Expect = 0.81
Identities = 13/67 (19%), Positives = 19/67 (28%)
Query: 82 LPIQQQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQQLLSGS 141
LP Q + VQ + Q V AP +T V + S
Sbjct: 376 LPEGQTPSALAAAVQAPHANEPQFVNAAPAEKKTALTEQTTAQQQVQAANAEAVAEADAS 435
Query: 142 HKSAEVT 148
+ A+
Sbjct: 436 AEPADTV 442
>gnl|CDD|198284 cd10421, SH2_STAT5a, Src homology 2 (SH2) domain found in signal
transducer and activator of transcription (STAT) 5a
proteins. STAT5 is a member of the STAT family of
transcription factors. Two highly related proteins,
STAT5a and STAT5b are encoded by separate genes, but are
90% identical at the amino acid level. Both STAT5a and
STAT5b are ubiquitously expressed and functionally
interchangeable. Mice lacking either STAT5a or STAT5b
have mild defects in prolactin dependent mammary
differentiation or sexually dimorphic growth
hormone-dependent effects, respectively. Mice lacking
both STAT5a and STAT5b exhibit a perinatal lethal
phenotype and have multiple defects, including anemia
and a virtual absence of B and T lymphocytes. STAT
proteins mediate the signaling of cytokines and a number
of growth factors from the receptors of these
extracellular signaling molecules to the cell nucleus.
STATs are specifically phosphorylated by
receptor-associated Janus kinases, receptor tyrosine
kinases, or cytoplasmic tyrosine kinases. The
phosphorylated STAT molecules dimerize by reciprocal
binding of their SH2 domains to the phosphotyrosine
residues. These dimeric STATs translocate into the
nucleus, bind to specific DNA sequences, and regulate
the transcription of their target genes. However there
are a number of unphosphorylated STATs that travel
between the cytoplasm and nucleus and some STATs that
exist as dimers in unstimulated cells that can exert
biological functions independent of being activated.
There are seven mammalian STAT family members which have
been identified: STAT1, STAT2, STAT3, STAT4, STAT5
(STAT5A and STAT5B), and STAT6. There are 6 conserved
domains in STAT: N-terminal domain (NTD), coiled-coil
domain (CCD), DNA-binding domain (DBD), alpha-helical
linker domain (LD), SH2 domain, and transactivation
domain (TAD). NTD is involved in dimerization of
unphosphorylated STATs monomers and for the
tetramerization between STAT1, STAT3, STAT4 and STAT5 on
promoters with two or more tandem STAT binding sites.
It also plays a role in promoting interactions with
transcriptional co-activators such as CREB binding
protein (CBP)/p300, as well as being important for
nuclear import and deactivation of STATs involving
tyrosine de-phosphorylation. CCD interacts with other
proteins, such as IFN regulatory protein 9 (IRF-9/p48)
with STAT1 and c-JUN with STAT3 and is also thought to
participate in the negative regulation of these
proteins. Distinct genes are bound to STATs via their
DBD domain. This domain is also involved in nuclear
translocation of activated STAT1 and STAT3
phosphorylated dimers upon cytokine stimulation. LD
links the DNA-binding and SH2 domains and is important
for the transcriptional activation of STAT1 in response
to IFN-gamma. It also plays a role in protein-protein
interactions and has also been implicated in the
constitutive nucleocytoplasmic shuttling of
unphosphorylated STATs in resting cells. The SH2 domain
is necessary for receptor association and tyrosine
phosphodimer formation. Residues within this domain may
be particularly important for some cellular functions
mediated by the STATs as well as residues adjacent to
this domain. The TAD interacts with several proteins,
namely minichromosome maintenance complex component 5
(MCM5), breast cancer 1 (BRCA1) and CBP/p300. TAD also
contains a modulatory phosphorylation site that
regulates STAT activity and is necessary for maximal
transcription of a number of target genes. The conserved
tyrosine residue present in the C-terminus is crucial
for dimerization via interaction with the SH2 domain
upon the interaction of the ligand with the receptor.
STAT activation by tyrosine phosphorylation also
determines nuclear import and retention, DNA binding to
specific DNA elements in the promoters of responsive
genes, and transcriptional activation of STAT dimers. In
addition to the SH2 domain there is a coiled-coil
domain, a DNA binding domain, and a transactivation
domain in the STAT proteins. In general SH2 domains are
involved in signal transduction. They typically bind
pTyr-containing ligands via two surface pockets, a pTyr
and hydrophobic binding pocket, allowing proteins with
SH2 domains to localize to tyrosine phosphorylated
sites.
Length = 140
Score = 28.9 bits (64), Expect = 0.88
Identities = 19/72 (26%), Positives = 28/72 (38%), Gaps = 7/72 (9%)
Query: 27 DSPSGNKWTAEDIEMLKETVRKFGDEL-------VIISDRIKDRTISQIKSNLKKKAFED 79
DSP N W + ++R D L + DR KD S+ + + KA +
Sbjct: 62 DSPDRNLWNLKPFTTRDFSIRSLADRLGDLNYLIYVFPDRPKDEVFSKYYTPVLAKAVDG 121
Query: 80 AGLPIQQQVAPP 91
P +QV P
Sbjct: 122 YVKPQIKQVVPE 133
>gnl|CDD|165132 PHA02767, PHA02767, hypothetical protein; Provisional.
Length = 101
Score = 28.4 bits (63), Expect = 0.91
Identities = 15/36 (41%), Positives = 20/36 (55%), Gaps = 9/36 (25%)
Query: 49 FGDELVIISDRIKDRTISQIKSNLKKKAFEDAGLPI 84
F DE +I+ QIK N+KKK +E AG+ I
Sbjct: 34 FEDEEIILI---------QIKINMKKKEYEKAGMSI 60
>gnl|CDD|236669 PRK10263, PRK10263, DNA translocase FtsK; Provisional.
Length = 1355
Score = 29.7 bits (66), Expect = 0.95
Identities = 17/51 (33%), Positives = 17/51 (33%)
Query: 85 QQQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQ 135
QQ VAP Q Q Q Q PQ P QQ V QQ
Sbjct: 782 QQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQ 832
Score = 29.3 bits (65), Expect = 1.6
Identities = 20/54 (37%), Positives = 21/54 (38%), Gaps = 3/54 (5%)
Query: 85 QQQVAPPQQIVQ---QVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQ 135
QQ VAP Q Q V Q Q Q P Q + QQ VA P QQ
Sbjct: 769 QQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQ 822
Score = 27.4 bits (60), Expect = 6.6
Identities = 22/72 (30%), Positives = 25/72 (34%), Gaps = 4/72 (5%)
Query: 86 QQVAPPQQIVQQVVQ----QQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQQLLSGS 141
QQ PQ QQ Q Q Q Q P Q + QQ VA P QQ +
Sbjct: 782 QQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQPQYQQPQQPVAPQP 841
Query: 142 HKSAEVTLNMLN 153
+ L M N
Sbjct: 842 QDTLLHPLLMRN 853
>gnl|CDD|237874 PRK14971, PRK14971, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 614
Score = 29.4 bits (66), Expect = 1.0
Identities = 13/64 (20%), Positives = 15/64 (23%), Gaps = 1/64 (1%)
Query: 86 QQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVA-TVPVPVSAQQQLLSGSHKS 144
Q A PQ Q A Q + TV V A + S
Sbjct: 385 QPAAAPQPSAAAAASPSPSQSSAAAQPSAPQSATQPAGTPPTVSVDPPAAVPVNPPSTAP 444
Query: 145 AEVT 148
V
Sbjct: 445 QAVR 448
>gnl|CDD|99734 cd00609, AAT_like, Aspartate aminotransferase family. This family
belongs to pyridoxal phosphate (PLP)-dependent aspartate
aminotransferase superfamily (fold I). Pyridoxal
phosphate combines with an alpha-amino acid to form a
compound called a Schiff base or aldimine intermediate,
which depending on the reaction, is the substrate in
four kinds of reactions (1) transamination (movement of
amino groups), (2) racemization (redistribution of
enantiomers), (3) decarboxylation (removing COOH
groups), and (4) various side-chain reactions depending
on the enzyme involved. Pyridoxal phosphate (PLP)
dependent enzymes were previously classified into alpha,
beta and gamma classes, based on the chemical
characteristics (carbon atom involved) of the reaction
they catalyzed. The availability of several structures
allowed a comprehensive analysis of the evolutionary
classification of PLP dependent enzymes, and it was
found that the functional classification did not always
agree with the evolutionary history of these enzymes.
The major groups in this CD corresponds to Aspartate
aminotransferase a, b and c, Tyrosine, Alanine,
Aromatic-amino-acid, Glutamine phenylpyruvate,
1-Aminocyclopropane-1-carboxylate synthase,
Histidinol-phosphate, gene products of malY and cobC,
Valine-pyruvate aminotransferase and Rhizopine
catabolism regulatory protein.
Length = 350
Score = 29.2 bits (66), Expect = 1.1
Identities = 13/34 (38%), Positives = 22/34 (64%), Gaps = 2/34 (5%)
Query: 25 TPDSPSGNKWTAEDIEMLKETVRKFGDELVIISD 58
P++P+G + E++E L E +K G ++IISD
Sbjct: 140 NPNNPTGAVLSEEELEELAELAKKHG--ILIISD 171
>gnl|CDD|200370 TIGR04119, CXXX_matur, CXXX repeat peptide maturase. This model
describes a peptide maturase that works with, usually
fused to, a radical SAM enzyme in a system that
modifies peptides with multiple tandem repeats of CXXX
sequences. This protein includes an iron-sulfur cluster
binding region associated with peptide modification as
described in domain model TIGR04085.
Length = 210
Score = 28.8 bits (65), Expect = 1.2
Identities = 16/63 (25%), Positives = 25/63 (39%), Gaps = 22/63 (34%)
Query: 32 NKWTAEDIEMLKETVRKFGD------------ELVIISDRIKDRTISQIKSNLKKKAFED 79
+KW D+++ K + K D E+ +I+DR+ LKK D
Sbjct: 36 DKWNNFDLDLYKSQLAKISDYIADLYKKGIIKEINVITDRL----------MLKKMNNCD 85
Query: 80 AGL 82
AG
Sbjct: 86 AGE 88
>gnl|CDD|220392 pfam09770, PAT1, Topoisomerase II-associated protein PAT1. Members
of this family are necessary for accurate chromosome
transmission during cell division.
Length = 804
Score = 29.4 bits (66), Expect = 1.2
Identities = 17/58 (29%), Positives = 18/58 (31%), Gaps = 5/58 (8%)
Query: 82 LPIQQQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQQLLS 139
L Q QQ+ Q QQ Q PQ P Q T P P Q Q
Sbjct: 243 LQQPQFPGLSQQMPPPPPQPPQQQ-QQPPQPQAQPPPQNQPT----PHPGLPQGQNAP 295
Score = 29.0 bits (65), Expect = 1.5
Identities = 17/60 (28%), Positives = 18/60 (30%), Gaps = 3/60 (5%)
Query: 82 LPIQQQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRV---VQQTVATVPVPVSAQQQLL 138
P Q PP QQQ Q P PT Q A +P P Q L
Sbjct: 248 FPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAPLPPPQQPQLLPL 307
Score = 29.0 bits (65), Expect = 1.8
Identities = 18/78 (23%), Positives = 20/78 (25%), Gaps = 3/78 (3%)
Query: 80 AGLPIQQQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQQLLS 139
P Q AP Q Q + Q Q Q Q P Q P QQ
Sbjct: 213 QVQPQQFLPAPSQAPAQPPLPPQLPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQP 272
Query: 140 GSHKSAEVTLNMLNAHPE 157
+ N HP
Sbjct: 273 QAQPPP---QNQPTPHPG 287
Score = 29.0 bits (65), Expect = 1.9
Identities = 10/41 (24%), Positives = 15/41 (36%)
Query: 83 PIQQQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQT 123
Q Q AP Q + QQ + Q ++VQ +
Sbjct: 288 LPQGQNAPLPPPQQPQLLPLVQQPQGQQRGPQFREQLVQLS 328
Score = 27.4 bits (61), Expect = 4.8
Identities = 12/62 (19%), Positives = 13/62 (20%)
Query: 82 LPIQQQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQQLLSGS 141
LP Q Q Q Q Q P Q P P Q +
Sbjct: 236 LPQQPPPLQQPQFPGLSQQMPPPPPQPPQQQQQPPQPQAQPPPQNQPTPHPGLPQGQNAP 295
Query: 142 HK 143
Sbjct: 296 LP 297
>gnl|CDD|173845 cd01156, IVD, Isovaleryl-CoA dehydrogenase. Isovaleryl-CoA
dehydrogenase (IVD) is an is an acyl-CoA dehydrogenase,
which catalyzes the third step in leucine catabolism,
the conversion of isovaleryl-CoA (3-methylbutyryl-CoA)
into 3-methylcrotonyl-CoA. IVD is a homotetramer and
has the greatest affinity for small branched chain
substrates.
Length = 376
Score = 28.5 bits (64), Expect = 1.8
Identities = 11/29 (37%), Positives = 21/29 (72%), Gaps = 2/29 (6%)
Query: 37 EDIEMLKETVRKFG-DELVIISDRIKDRT 64
++IEML+++VR+F E+ ++ +I DR
Sbjct: 4 DEIEMLRQSVREFAQKEIAPLAAKI-DRD 31
>gnl|CDD|236444 PRK09275, PRK09275, aspartate aminotransferase; Provisional.
Length = 527
Score = 28.7 bits (65), Expect = 1.9
Identities = 9/33 (27%), Positives = 18/33 (54%)
Query: 26 PDSPSGNKWTAEDIEMLKETVRKFGDELVIISD 58
P +P + E +E + + V + +L+II+D
Sbjct: 250 PSNPPSVAMSDESLEKIADIVNEKRPDLMIITD 282
>gnl|CDD|162743 TIGR02172, Fb_sc_TIGR02172, Fibrobacter succinogenes paralogous
family TIGR02172. This model describes a paralogous
family of five proteins, likely to be enzymes, in the
rumen bacterium Fibrobacter succinogenes S85. Members
show homology to proteins described by pfam01636, a
phosphotransferase enzyme family associated with
resistance to aminoglycoside antibiotics. However,
members of this family score below the current trusted
and noise cutoffs for pfam01636.
Length = 226
Score = 28.2 bits (63), Expect = 1.9
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 7/56 (12%)
Query: 15 LADLTLQLHSTPDSPSGNKWTAEDIEMLKETVRKFGDELVIISDRIKDRTISQIKS 70
A++ +LHST S + KE +RKF +E + K++ + IK
Sbjct: 100 FAEMAKKLHSTKCDTSTFQSY-------KEKIRKFIEEKDFVPKDYKEKARAFIKE 148
>gnl|CDD|240336 PTZ00260, PTZ00260, dolichyl-phosphate beta-glucosyltransferase;
Provisional.
Length = 333
Score = 28.6 bits (64), Expect = 1.9
Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 10/54 (18%)
Query: 41 MLKETVR----------KFGDELVIISDRIKDRTISQIKSNLKKKAFEDAGLPI 84
MLKET++ KF E++I++D KD+T+ K ++ + + +
Sbjct: 88 MLKETIKYLESRSRKDPKFKYEIIIVNDGSKDKTLKVAKDFWRQNINPNIDIRL 141
>gnl|CDD|221503 pfam12275, DUF3616, Protein of unknown function (DUF3616). This
family of proteins is found in bacteria. Proteins in
this family are typically between 335 and 392 amino
acids in length. There is a conserved GLRGPV sequence
motif.
Length = 331
Score = 28.5 bits (64), Expect = 2.1
Identities = 15/44 (34%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 125 ATVP--VPVSAQQQLLSGSHKSAEV-TLNMLNAHPESEVDVEGL 165
AT+ V + A ++ G HKS + L P+ E D+EGL
Sbjct: 21 ATIERLVLLEAGGRVRFGGHKSFPLGDFFDLPGEPDKEADIEGL 64
>gnl|CDD|215756 pfam00155, Aminotran_1_2, Aminotransferase class I and II.
Length = 357
Score = 28.4 bits (64), Expect = 2.1
Identities = 10/37 (27%), Positives = 23/37 (62%), Gaps = 2/37 (5%)
Query: 22 LHSTPDSPSGNKWTAEDIEMLKETVRKFGDELVIISD 58
LH++P +P+G T E++E L + ++ ++++ D
Sbjct: 147 LHTSPHNPTGTVATLEELEKLLDLAKEHN--ILLLVD 181
>gnl|CDD|222095 pfam13388, DUF4106, Protein of unknown function (DUF4106). This
family of proteins are found in large numbers in the
Trichomonas vaginalis proteome. The function of this
protein is unknown.
Length = 422
Score = 28.5 bits (63), Expect = 2.2
Identities = 14/47 (29%), Positives = 15/47 (31%)
Query: 90 PPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQQ 136
P QQ Q QQ A Q Q P + Q AQQ
Sbjct: 203 PTQQPTVQNPAQQPTVQNPAQQPQQQPQQQPVQPAQQPTPQNPAQQP 249
Score = 26.6 bits (58), Expect = 8.3
Identities = 18/62 (29%), Positives = 20/62 (32%), Gaps = 4/62 (6%)
Query: 85 QQQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQQLLSGSHKS 144
QQ Q VQ QQ Q Q P + QQ T P Q G +S
Sbjct: 204 TQQPTVQNPAQQPTVQNPAQQ--PQQQPQQQPVQPAQQ--PTPQNPAQQPPQTEQGHKRS 259
Query: 145 AE 146
E
Sbjct: 260 RE 261
>gnl|CDD|172952 PRK14477, PRK14477, bifunctional nitrogenase molybdenum-cofactor
biosynthesis protein NifE/NifN; Provisional.
Length = 917
Score = 28.6 bits (64), Expect = 2.2
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 31 GNKWTAEDIEMLKETVRKFGDELVIISD 58
G T D+E +KE V FG + V++ D
Sbjct: 652 GAHLTPADVEEIKEIVEAFGLDPVVVPD 679
>gnl|CDD|165711 PLN00143, PLN00143, tyrosine/nicotianamine aminotransferase;
Provisional.
Length = 409
Score = 28.4 bits (63), Expect = 2.4
Identities = 11/35 (31%), Positives = 22/35 (62%), Gaps = 2/35 (5%)
Query: 26 PDSPSGNKWTAEDIEMLKETVRKFGDELVIISDRI 60
P +P G+ ++ E + + ET RK G +++I+D +
Sbjct: 179 PGNPCGSVYSYEHLNKIAETARKLG--ILVIADEV 211
>gnl|CDD|183514 PRK12414, PRK12414, putative aminotransferase; Provisional.
Length = 384
Score = 28.2 bits (63), Expect = 2.6
Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 25 TPDSPSGNKWTAEDIEMLKETVRKFGDELVIISDRI 60
TP +PS ++A D+ L + R ++VI+SD +
Sbjct: 170 TPHNPSATVFSAADLARLAQLTR--NTDIVILSDEV 203
>gnl|CDD|202808 pfam03920, TLE_N, Groucho/TLE N-terminal Q-rich domain. The
N-terminal domain of the Grouch/TLE co-repressor
proteins are involved in oligomerisation.
Length = 134
Score = 27.1 bits (60), Expect = 3.3
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 6/51 (11%)
Query: 92 QQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQQLLSGSH 142
QI+ + Q+ QQV QA + R Q T+A + + Q Q SH
Sbjct: 89 AQILPFLSQEHQQQVAQAVE------RAKQVTMAELNAIIGQQLQAQQLSH 133
>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 926
Score = 28.0 bits (62), Expect = 3.4
Identities = 11/49 (22%), Positives = 21/49 (42%), Gaps = 3/49 (6%)
Query: 46 VRKFGDELVIISDRIKDRTISQIKSNLKKKAFEDAGLPIQQQVAPPQQI 94
VRKF +V++ DR ++ I++ + K D P+ +
Sbjct: 876 VRKFKGGVVVLRDREPKEPVALIETVRQMK---DVNAPLPTPFKVDDNV 921
>gnl|CDD|223157 COG0079, HisC, Histidinol-phosphate/aromatic aminotransferase and
cobyric acid decarboxylase [Amino acid transport and
metabolism].
Length = 356
Score = 27.7 bits (62), Expect = 4.1
Identities = 10/33 (30%), Positives = 18/33 (54%), Gaps = 2/33 (6%)
Query: 24 STPDSPSGNKWTAEDIEMLKETVRKFGDELVII 56
P++P+G E++ L E + + G LV+I
Sbjct: 152 CNPNNPTGTLLPREELRALLEALPEGG--LVVI 182
>gnl|CDD|118654 pfam10126, Nit_Regul_Hom, Uncharacterized protein, homolog of
nitrogen regulatory protein PII. This domain, found in
various hypothetical archaeal proteins, has no known
function. It is distantly similar to the nitrogen
regulatory protein PII.
Length = 110
Score = 26.6 bits (59), Expect = 4.5
Identities = 11/40 (27%), Positives = 22/40 (55%)
Query: 36 AEDIEMLKETVRKFGDELVIISDRIKDRTISQIKSNLKKK 75
ED EM + +R ++ V+I+ + + + +I LK+K
Sbjct: 50 REDPEMAIKAIRDLSEDAVMINTVVSEEKVEKIVELLKEK 89
>gnl|CDD|235285 PRK04335, PRK04335, cell division protein ZipA; Provisional.
Length = 313
Score = 27.5 bits (61), Expect = 4.6
Identities = 26/129 (20%), Positives = 43/129 (33%), Gaps = 9/129 (6%)
Query: 12 FNKLADLTLQLHSTPDSPSGNKWTAEDIEMLKETVRK------FGDELVIISDRIKDRTI 65
F L + S + P+ + A+ E E +RK FG E I D
Sbjct: 35 FGDKPLGKLDVDSDDEQPAPERGFAQAPEDDFEIIRKERKEPDFGRENSFHDPLIDDPLF 94
Query: 66 SQIKSN-LKKKAFEDAGLPIQQQVAPPQQIVQQVVQQQHQQVV--QAPQMVQTPTRVVQQ 122
K E+A +P+Q Q P + V+ V++ + V + + Q
Sbjct: 95 GGELEEEEDKFEQEEAPIPVQAQSQPQPEKVEPQVEEPRDEEVLEEPEPVAAKVPMAEVQ 154
Query: 123 TVATVPVPV 131
+ V
Sbjct: 155 PEEETEIEV 163
>gnl|CDD|237264 PRK13007, PRK13007, succinyl-diaminopimelate desuccinylase;
Reviewed.
Length = 352
Score = 27.1 bits (61), Expect = 5.0
Identities = 12/24 (50%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 142 HKSAEVTLNMLNAHPESEVDVEGL 165
HK+A V L L A+ EV V+GL
Sbjct: 192 HKAAPV-LARLAAYEPREVVVDGL 214
>gnl|CDD|180720 PRK06836, PRK06836, aspartate aminotransferase; Provisional.
Length = 394
Score = 27.1 bits (61), Expect = 5.1
Identities = 10/38 (26%), Positives = 25/38 (65%), Gaps = 4/38 (10%)
Query: 25 TPDSPSGNKWTAEDIE----MLKETVRKFGDELVIISD 58
+P++P+G ++ E ++ +L+E +++G + +ISD
Sbjct: 176 SPNNPTGVVYSEETLKALAALLEEKSKEYGRPIYLISD 213
>gnl|CDD|227448 COG5118, BDP1, Transcription initiation factor TFIIIB, Bdp1 subunit
[Transcription].
Length = 507
Score = 27.4 bits (60), Expect = 5.2
Identities = 11/44 (25%), Positives = 23/44 (52%)
Query: 33 KWTAEDIEMLKETVRKFGDELVIISDRIKDRTISQIKSNLKKKA 76
+W+ ++IE + + +G + +IS +R QIK+ K+
Sbjct: 367 RWSKKEIEKFYKALSIWGTDFSLISSLFPNRERKQIKAKFIKEE 410
>gnl|CDD|219339 pfam07223, DUF1421, Protein of unknown function (DUF1421). This
family represents a conserved region approximately 350
residues long within a number of plant proteins of
unknown function.
Length = 357
Score = 27.2 bits (60), Expect = 5.7
Identities = 15/45 (33%), Positives = 16/45 (35%)
Query: 84 IQQQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVP 128
Q Q PQ Q QQQ+Q Q PQ Q P Q
Sbjct: 134 QQPQAQQPQPPPQVPQQQQYQSPPQQPQYQQNPPPQAQSAPQVSG 178
>gnl|CDD|234275 TIGR03599, YloV, DAK2 domain fusion protein YloV. This model
describes a protein family that contains an N-terminal
DAK2 domain (pfam02734), so named because of similarity
to the dihydroxyacetone kinase family family. The
GTP-binding protein CgtA (a member of the obg family) is
a bacterial GTPase associated with ribosome biogenesis,
and it has a characteristic extension (TIGR03595) in
certain lineages. This protein family described here was
found, by the method of partial phylognetic profiling,
to have a phylogenetic distribution strongly correlated
to that of TIGR03595. This correlation implies some form
of functional coupling.
Length = 530
Score = 27.1 bits (61), Expect = 6.0
Identities = 8/23 (34%), Positives = 13/23 (56%)
Query: 36 AEDIEMLKETVRKFGDELVIISD 58
D E ++ + K GD LV++ D
Sbjct: 236 KFDEEKFRKELEKLGDSLVVVGD 258
>gnl|CDD|234547 TIGR04330, cas_Cpf1, CRISPR-associated protein Cpf1, subtype PREFRAN.
This family is the long protein of a novel CRISPR
subtype, PREFRAN, which is most common in Prevotella and
Francisella, although widely distributed. The PREFRAN
type has Cas1, Cas2, and Cas4, but lacks the helicase
Cas3 and endonuclease Cas3-HD.
Length = 1287
Score = 27.1 bits (60), Expect = 6.1
Identities = 12/53 (22%), Positives = 18/53 (33%), Gaps = 2/53 (3%)
Query: 27 DSPSGNKWTAEDIEMLKETVRKFGDELVIISDRIKDRTISQIKSNLKKKAFED 79
+ N W E+I + +E D + D + I KK F D
Sbjct: 1144 NKDKNNYWDTEEINLTEEIKALLEDNAINYGDGNCIKE--AIAGKSDKKFFAD 1194
>gnl|CDD|237466 PRK13674, PRK13674, putative GTP cyclohydrolase; Provisional.
Length = 271
Score = 26.7 bits (60), Expect = 6.2
Identities = 19/56 (33%), Positives = 21/56 (37%), Gaps = 3/56 (5%)
Query: 110 PQMVQTPTRVVQQTVATVPVPVSAQQQLLSGSHKSAEVTLNMLNAHPESEVDVEGL 165
P V T Q TVA V + VS G H S L L H E E+ L
Sbjct: 34 PVRVDTRDGGTQTTVARVDLTVSLPAD-FKGIHMSRLYEL--LEEHAEQELSPASL 86
>gnl|CDD|233290 TIGR01141, hisC, histidinol-phosphate aminotransferase. Alternate
names: histidinol-phosphate transaminase; imidazole
acetol-phosphate transaminase Histidinol-phosphate
aminotransferase is a pyridoxal-phosphate dependent
enzyme [Amino acid biosynthesis, Histidine family].
Length = 346
Score = 26.8 bits (60), Expect = 6.3
Identities = 11/32 (34%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 25 TPDSPSGNKWTAEDIEMLKETVRKFGDELVII 56
+P++P+GN + DIE + E D LV++
Sbjct: 150 SPNNPTGNLLSRSDIEAVLERTP--EDALVVV 179
>gnl|CDD|185309 PRK15411, rcsA, colanic acid capsular biosynthesis activation
protein A; Provisional.
Length = 207
Score = 26.6 bits (59), Expect = 6.3
Identities = 11/22 (50%), Positives = 16/22 (72%), Gaps = 2/22 (9%)
Query: 56 ISDR--IKDRTISQIKSNLKKK 75
ISD+ IK +T+S K N+K+K
Sbjct: 158 ISDQMNIKAKTVSSHKGNIKRK 179
>gnl|CDD|237722 PRK14476, PRK14476, nitrogenase molybdenum-cofactor biosynthesis
protein NifN; Provisional.
Length = 455
Score = 27.1 bits (61), Expect = 6.4
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 35 TAEDIEMLKETVRKFGDELVIISD 58
T DIE L+E + FG E +I+ D
Sbjct: 180 TPGDIEELREIIEAFGLEPIILPD 203
>gnl|CDD|163513 TIGR03801, asp_4_decarbox, aspartate 4-decarboxylase. This enzyme,
aspartate 4-decarboxylase (EC 4.1.1.12), removes the
side-chain carboxylate from L-aspartate, converting it
to L-alanine plus carbon dioxide. It is a PLP-dependent
enzyme, homologous to aspartate aminotransferase (EC
2.6.1.1) [Energy metabolism, Amino acids and amines].
Length = 521
Score = 26.9 bits (60), Expect = 6.6
Identities = 9/33 (27%), Positives = 17/33 (51%)
Query: 26 PDSPSGNKWTAEDIEMLKETVRKFGDELVIISD 58
P +P + E IE + + V +L+I++D
Sbjct: 249 PSNPPSVAMSDESIEKIVDIVANDRPDLMILTD 281
>gnl|CDD|146221 pfam03465, eRF1_3, eRF1 domain 3. The release factor eRF1
terminates protein biosynthesis by recognising stop
codons at the A site of the ribosome and stimulating
peptidyl-tRNA bond hydrolysis at the peptidyl
transferase centre. The crystal structure of human eRF1
is known. The overall shape and dimensions of eRF1
resemble a tRNA molecule with domains 1, 2, and 3 of
eRF1 corresponding to the anticodon loop, aminoacyl
acceptor stem, and T stem of a tRNA molecule,
respectively. The position of the essential GGQ motif
at an exposed tip of domain 2 suggests that the Gln
residue coordinates a water molecule to mediate the
hydrolytic activity at the peptidyl transferase centre.
A conserved groove on domain 1, 80 A from the GGQ
motif, is proposed to form the codon recognition site.
This family also includes other proteins for which the
precise molecular function is unknown. Many of them are
from Archaebacteria. These proteins may also be
involved in translation termination but this awaits
experimental verification.
Length = 100
Score = 25.6 bits (57), Expect = 6.9
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 37 EDIEMLKETVRKFGDELVIISDR 59
IE L E + G ++ I+SD
Sbjct: 57 NKIEWLVENAEESGGKVEIVSDE 79
>gnl|CDD|220309 pfam09606, Med15, ARC105 or Med15 subunit of Mediator complex
non-fungal. The approx. 70 residue Med15 domain of the
ARC-Mediator co-activator is a three-helix bundle with
marked similarity to the KIX domain. The sterol
regulatory element binding protein (SREBP) family of
transcription activators use the ARC105 subunit to
activate target genes in the regulation of cholesterol
and fatty acid homeostasis. In addition, Med15 is a
critical transducer of gene activation signals that
control early metazoan development.
Length = 768
Score = 26.9 bits (59), Expect = 7.1
Identities = 19/58 (32%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 83 PIQQQVAPPQQIVQQVVQQQHQQVVQA---PQMVQTPTRVVQQTVATVPVPVSAQQQL 137
P Q P Q +QQQ Q Q PQM Q QQ + P AQ Q+
Sbjct: 194 PQMGQPGMPGGGGQGQMQQQGQPGGQQQQNPQMQQQLQNQQQQQMDQQQGPADAQAQM 251
>gnl|CDD|217220 pfam02771, Acyl-CoA_dh_N, Acyl-CoA dehydrogenase, N-terminal
domain. The N-terminal domain of Acyl-CoA
dehydrogenase is an all-alpha domain.
Length = 113
Score = 25.9 bits (58), Expect = 7.2
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 37 EDIEMLKETVRKFGDE 52
E+ E L++TVR+F +E
Sbjct: 2 EEQEALRDTVREFAEE 17
>gnl|CDD|234022 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid
synthase PfaA. Members of the seed for this alignment
are involved in omega-3 polyunsaturated fatty acid
biosynthesis, such as the protein PfaA from the
eicosapentaenoic acid biosynthesis operon in
Photobacterium profundum strain SS9. PfaA is encoded
together with PfaB, PfaC, and PfaD, and the functions of
the individual polypeptides have not yet been described.
More distant homologs of PfaA, also included with the
reach of this model, appear to be involved in
polyketide-like biosynthetic mechanisms of
polyunsaturated fatty acid biosynthesis, an alternative
to the more familiar iterated mechanism of chain
extension and desaturation, and in most cases are encoded
near genes for homologs of PfaB, PfaC, and/or PfaD.
Length = 2582
Score = 26.9 bits (59), Expect = 7.6
Identities = 12/54 (22%), Positives = 18/54 (33%), Gaps = 8/54 (14%)
Query: 83 PIQQQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPV---PVSA 133
P+ Q + VV P + P + V VA PV P++
Sbjct: 1137 PVVQVTISVAPAAPVLP-----AVVSPPVVSAAPAQSVATAVAMAPVAEVPIAV 1185
>gnl|CDD|221188 pfam11725, AvrE, Pathogenicity factor. This family is secreted by
gram-negative Gammaproteobacteria such as Pseudomonas
syringae of tomato and the fire blight plant pathogen
Erwinia amylovora, amongst others. It is an essential
pathogenicity factor of approximately 198 kDa. Its
injection into the host-plant is dependent upon the
bacterial type III or Hrp secretion system. The family
is long and carries a number of predicted functional
regions, including an ERMS or endoplasmic reticulum
membrane retention signal at both the C- and the
N-termini, a leucine-zipper motif from residues 539-560,
and a nuclear localisation signal at 1358-1361. this
conserved AvrE-family of effectors is among the few that
are required for full virulence of many phytopathogenic
pseudomonads, erwinias and pantoeas.
Length = 1771
Score = 26.7 bits (59), Expect = 8.4
Identities = 19/103 (18%), Positives = 36/103 (34%), Gaps = 3/103 (2%)
Query: 79 DAGLPIQQQVAPPQQIVQQVVQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQQLL 138
A +QQ P Q + + ++ + V + +Q A P ++
Sbjct: 23 GAPTGLQQSSESPTQRASHSLASEGKKNRKKMPKVFQKSSAPRQIQAAPPQALNPTA--- 79
Query: 139 SGSHKSAEVTLNMLNAHPESEVDVEGLPEEVKLQFDTTAQQVA 181
+ S TL L A PE + + + + T ++ VA
Sbjct: 80 AAPQSSRGPTLRELLALPEDDGETQAPESSPSARRLTRSEGVA 122
>gnl|CDD|237361 PRK13355, PRK13355, bifunctional HTH-domain containing
protein/aminotransferase; Provisional.
Length = 517
Score = 26.6 bits (59), Expect = 8.9
Identities = 12/38 (31%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 26 PDSPSGNKWTAEDIEMLKETVRKFGDELVIISDRIKDR 63
P++P+G + E ++ + + R+ +L+I SD I DR
Sbjct: 290 PNNPTGALYPREVLQQIVDIAREH--QLIIFSDEIYDR 325
>gnl|CDD|234977 PRK01741, PRK01741, cell division protein ZipA; Provisional.
Length = 332
Score = 26.6 bits (59), Expect = 9.0
Identities = 15/125 (12%), Positives = 36/125 (28%), Gaps = 5/125 (4%)
Query: 44 ETVRKFGDELVIISDRIKDRTISQIKSNLKKKAF-----EDAGLPIQQQVAPPQQIVQQV 98
+ E + + ++++ +IK L + PIQ Q Q
Sbjct: 77 PQTEESESENEVQIQQEVEQSVDEIKITLPNQEPAYYMQNHRSEPIQPTQPQYQSPTQTN 136
Query: 99 VQQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQQLLSGSHKSAEVTLNMLNAHPES 158
V + Q+P + + + ++A+ + A E+
Sbjct: 137 VASMTIEETQSPNVPIEGINSSSEQLRVELAELAAEIYSDASHRVELAKNFMEPQAETEA 196
Query: 159 EVDVE 163
+ +
Sbjct: 197 QPEAT 201
>gnl|CDD|182312 PRK10216, PRK10216, DNA-binding transcriptional regulator YidZ;
Provisional.
Length = 319
Score = 26.3 bits (58), Expect = 9.0
Identities = 10/37 (27%), Positives = 17/37 (45%)
Query: 100 QQQHQQVVQAPQMVQTPTRVVQQTVATVPVPVSAQQQ 136
Q H + AP+ Q ++ Q + +P+P QQ
Sbjct: 247 QPDHLLLATAPRYCQYYNQLHQLPLVALPLPFDESQQ 283
>gnl|CDD|233628 TIGR01900, dapE-gram_pos, succinyl-diaminopimelate desuccinylase.
This model represents a clade of
succinyl-diaminopimelate desuccinylases from
actinobacteria (high-GC gram positives),
delta-proteobacteria and aquificales and is based on the
characterization of the enzyme from Corynebacterium
glutamicum. This enzyme is involved in the biosynthesis
of lysine, and is related to the enzyme acetylornithine
deacetylase and other amidases and peptidases found
within pfam01546. Other sequences included in the seed
of this model were assessed to confirm that 1) the
related genes DapC (succinyl-diaminopimelate
transaminase) and DapD
(2,3,4,5-tetrahydropyridine-2,6-dicarboxylate
N-succinyltransferase) are also found in the genome, 2)
each is found only once in those genomes, 3) the lysine
biosynthesis pathway is complete and 4) the direct
(TIGR03540 or TIGR03542) or acetylated (GenProp0787)
aminotransferase pathways are absent in thes genomes.
Additionally, a number of the seed members are observed
adjacent to either DapC or DapD (often as a divergon
with a putative promoter site between them [Amino acid
biosynthesis, Aspartate family].
Length = 351
Score = 26.5 bits (59), Expect = 9.1
Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 1/24 (4%)
Query: 142 HKSAEVTLNMLNAHPESEVDVEGL 165
HK+A + L L A+ EV V+GL
Sbjct: 190 HKAAPI-LARLAAYEPREVTVDGL 212
>gnl|CDD|211345 cd02868, PseudoU_synth_hTruB2_like, Pseudouridine synthase,
humanTRUB2_like. This group consists of eukaryotic
pseudouridine synthases similar to human TruB
pseudouridine synthase homolog 2 (TRUB2). Pseudouridine
synthases catalyze the isomerization of specific
uridines in an RNA molecule to pseudouridines
(5-ribosyluracil, psi).
Length = 226
Score = 26.2 bits (58), Expect = 9.4
Identities = 12/35 (34%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 55 IISDRIKDRTISQIKSNLKKKAFEDAGLPIQQQVA 89
I ++I +R ++ I+S ++KAFE + Q Q A
Sbjct: 99 ITREKI-ERLLAVIQSGHQQKAFELCSVDDQSQQA 132
>gnl|CDD|181580 PRK08912, PRK08912, hypothetical protein; Provisional.
Length = 387
Score = 26.5 bits (59), Expect = 9.7
Identities = 9/34 (26%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 25 TPDSPSGNKWTAEDIEMLKETVRKFGDELVIISD 58
P +P+G + E++ +L E ++ + V I D
Sbjct: 167 NPLNPAGKVFPREELALLAEFCQRH--DAVAICD 198
>gnl|CDD|225241 COG2366, COG2366, Protein related to penicillin acylase [General
function prediction only].
Length = 768
Score = 26.7 bits (59), Expect = 9.7
Identities = 11/34 (32%), Positives = 16/34 (47%)
Query: 62 DRTISQIKSNLKKKAFEDAGLPIQQQVAPPQQIV 95
D ++ + NL +FED G + PPQ V
Sbjct: 396 DEILACLLLNLAATSFEDFGNAAEYFAIPPQNWV 429
>gnl|CDD|238928 cd01966, Nitrogenase_NifN_1, Nitrogenase_nifN1: A subgroup of the
NifN subunit of the NifEN complex: NifN forms an
alpha2beta2 tetramer with NifE. NifN and nifE are
structurally homologous to nitrogenase MoFe protein beta
and alpha subunits respectively. NifEN participates in
the synthesis of the iron-molybdenum cofactor (FeMoco)
of the MoFe protein. NifB-co (an iron and sulfur
containing precursor of the FeMoco) from NifB is
transferred to the NifEN complex where it is further
processed to FeMoco. The nifEN bound precursor of FeMoco
has been identified as a molybdenum-free, iron- and
sulfur- containing analog of FeMoco. It has been
suggested that this nifEN bound precursor also acts as a
cofactor precursor in nitrogenase systems which require
a cofactor other than FeMoco: i.e. iron-vanadium
cofactor (FeVco) or iron only cofactor (FeFeco).
Length = 417
Score = 26.4 bits (59), Expect = 10.0
Identities = 10/24 (41%), Positives = 15/24 (62%)
Query: 35 TAEDIEMLKETVRKFGDELVIISD 58
T D+E LK+ + FG E +I+ D
Sbjct: 169 TPGDVEELKDIIEAFGLEPIILPD 192
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
0.312 0.126 0.342
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,937,856
Number of extensions: 803864
Number of successful extensions: 1544
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1300
Number of HSP's successfully gapped: 182
Length of query: 182
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 91
Effective length of database: 6,901,388
Effective search space: 628026308
Effective search space used: 628026308
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 56 (25.5 bits)