RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4529
(123 letters)
>gnl|CDD|238580 cd01175, IPT_COE, IPT domain of the COE family (Col/Olf-1/EBF) of
non-basic, helix-loop-helix (HLH)-containing
transcription factors. COE family proteins are all
transcription factors and play an important role in
variety of developmental processes. Mouse EBF is
involved in the regulation of the early stages of
B-cell differentiation, Drosophila collier is a
regulator of the head patterning, and a related protein
in Xenopus is involved in primary neurogenesis. All COE
family members have a well conserved DNA binding domain
that contains an atypical Zn finger motif. The function
of the IPT domain is unknown.
Length = 85
Score = 86.2 bits (213), Expect = 2e-23
Identities = 39/43 (90%), Positives = 40/43 (93%)
Query: 54 LITSHAIRVQTPPRHIPGVVEVTLSYKSKQFCKGAPGRFVYVS 96
LIT HAIRVQTPPRHIPGVVEVTLSYKSKQFCKG PGRFVY +
Sbjct: 43 LITPHAIRVQTPPRHIPGVVEVTLSYKSKQFCKGTPGRFVYTA 85
>gnl|CDD|239166 cd02765, MopB_4, The MopB_4 CD includes a group of related
uncharacterized bacterial and archaeal
molybdopterin-binding oxidoreductase-like domains with a
putative N-terminal iron-sulfur [4Fe-4S] cluster binding
site and molybdopterin cofactor binding site. These
members belong to the molybdopterin_binding (MopB)
superfamily of proteins.
Length = 567
Score = 29.8 bits (67), Expect = 0.31
Identities = 18/81 (22%), Positives = 28/81 (34%), Gaps = 18/81 (22%)
Query: 32 SPTSTPNSHFINANTSGWNHCTLITSHAIRVQTPPRHIPGVVEVTLSYKSKQFCKGAPGR 91
P P+ + CT SH RV +P R L Y K+ + G+
Sbjct: 27 EPNEWPDKTYKRG-------CTRGLSHLQRVYSPDR---------LKYPMKRVGERGEGK 70
Query: 92 FVYVSLNEP--TIDYGFQRLQ 110
F ++ +E TI +
Sbjct: 71 FERITWDEALDTIADKLTEAK 91
>gnl|CDD|225803 COG3264, COG3264, Small-conductance mechanosensitive channel [Cell
envelope biogenesis, outer membrane].
Length = 835
Score = 28.5 bits (64), Expect = 0.96
Identities = 9/29 (31%), Positives = 10/29 (34%)
Query: 37 PNSHFINANTSGWNHCTLITSHAIRVQTP 65
PNS FI W+ T I V
Sbjct: 697 PNSAFITEQVINWSLRDTTTRLVIPVGVA 725
>gnl|CDD|238050 cd00102, IPT, Immunoglobulin-like fold, Plexins, Transcription
factors (IPT). IPTs are also known as Transcription
factor ImmunoGlobin (TIG) domains. They are present in
intracellular transcription factors, cell surface
receptors (such as plexins and scatter factor
receptors), as well as, cyclodextrin
glycosyltransferase and similar enzymes. Although they
are involved in DNA binding in transcription factors,
their function in other proteins is unknown. In these
transcription factors, IPTs form homo- or heterodimers
with the exception of the nuclear factor of activated
Tcells (NFAT) transcription factors which are mainly
monomers.
Length = 89
Score = 26.7 bits (59), Expect = 1.5
Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 55 ITSHAIRVQTPPRHIPGVVEVTLSYKSK-QFCKGAPGRFVYVS 96
++S AI TPP PG V ++ +P F YV
Sbjct: 47 VSSTAIVCTTPPYANPGPGPVEVTVDRGNGGITSSPLTFTYVP 89
>gnl|CDD|237291 PRK13168, rumA, 23S rRNA m(5)U1939 methyltransferase; Reviewed.
Length = 443
Score = 27.4 bits (62), Expect = 1.9
Identities = 14/34 (41%), Positives = 15/34 (44%), Gaps = 7/34 (20%)
Query: 65 PPRHIPGVVEVTLSYKSKQFCKGAPGRFVYVSLN 98
PPR G EV + K P R VYVS N
Sbjct: 375 PPR--AGAAEV-----MQALAKLGPKRIVYVSCN 401
>gnl|CDD|129571 TIGR00479, rumA, 23S rRNA (uracil-5-)-methyltransferase RumA. This
protein family was first proposed to be RNA
methyltransferases by homology to the TrmA family. The
member from E. coli has now been shown to act as the 23S
RNA methyltransferase for the conserved U1939. The gene
is now designated rumA and was previously designated
ygcA [Protein synthesis, tRNA and rRNA base
modification].
Length = 431
Score = 27.1 bits (60), Expect = 3.0
Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 6/38 (15%)
Query: 65 PPRHIPGVVEVTLSYKSKQFCKGAPGRFVYVSLNEPTI 102
PPR G L + + P R VYVS N T+
Sbjct: 370 PPR--KGCAAEVL----RTIIELKPERIVYVSCNPATL 401
>gnl|CDD|233646 TIGR01936, nqrA, NADH:ubiquinone oxidoreductase,
Na(+)-translocating, A subunit. This model represents
the NqrA subunit of the six-protein, Na(+)-pumping
NADH-quinone reductase of a number of marine and
pathogenic Gram-negative bacteria. This oxidoreductase
complex functions primarily as a sodium ion pump
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 447
Score = 27.0 bits (60), Expect = 3.0
Identities = 13/56 (23%), Positives = 21/56 (37%), Gaps = 12/56 (21%)
Query: 1 LPTGSSYSYDHHTLSSDPDEKSAFI-----------PVTRASSPTSTPNSHFINAN 45
+ +YD TLS++ K + P ++P S+P FI A
Sbjct: 98 GEFATFPTYDLQTLSAE-QIKENLLESGLWTAIKQRPFDIVATPDSSPRDIFITAA 152
>gnl|CDD|202376 pfam02754, CCG, Cysteine-rich domain. The key element of this
family is the CX31-38CCX33-34CXXC sequence motif
normally found at the C-terminus in archaeal and
bacterial Hdr-like proteins. There may be one or two
copies, and the motif is probably an iron-sulfur
binding cluster. In some instances one of the cysteines
is replaced by an aspartate, and aspartate can in
principle also function as a ligand of an iron-sulfur
cluster. The family includes a subunit from
heterodisulphide reductase and a subunit from glycolate
oxidase and glycerol-3-phosphate dehydrogenase.
Length = 85
Score = 25.7 bits (57), Expect = 3.2
Identities = 11/40 (27%), Positives = 16/40 (40%), Gaps = 5/40 (12%)
Query: 58 HAIRVQTPP-----RHIPGVVEVTLSYKSKQFCKGAPGRF 92
H R P + + G + + + KQ C GA G F
Sbjct: 8 HLGRALYPEPRKALKKVLGALGIEVVILEKQSCCGAGGGF 47
>gnl|CDD|182669 PRK10714, PRK10714, undecaprenyl phosphate
4-deoxy-4-formamido-L-arabinose transferase;
Provisional.
Length = 325
Score = 26.6 bits (59), Expect = 3.2
Identities = 22/70 (31%), Positives = 32/70 (45%), Gaps = 12/70 (17%)
Query: 15 SSDPDEKSAFIPVTRASSPTSTPNSHFINAN-------TSGWNHCT--LITSHAIRVQTP 65
SSD SA + V A +P S + +N N +G++H T LI + +Q P
Sbjct: 48 SSD---NSAEMLVEAAQAPDSHIVAILLNRNYGQHSAIMAGFSHVTGDLIITLDADLQNP 104
Query: 66 PRHIPGVVEV 75
P IP +V
Sbjct: 105 PEEIPRLVAK 114
>gnl|CDD|233030 TIGR00575, dnlj, DNA ligase, NAD-dependent. All proteins in this
family with known functions are NAD-dependent DNA
ligases. Functions of these proteins include DNA repair,
DNA replication, and DNA recombination. This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University). The member of this
family from Treponema pallidum differs in having three
rather than just one copy of the BRCT (BRCA1 C Terminus)
domain (pfam00533) at the C-terminus. It is included in
the seed [DNA metabolism, DNA replication,
recombination, and repair].
Length = 652
Score = 26.9 bits (60), Expect = 3.6
Identities = 13/34 (38%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 94 YVSLNEPTI-----DYGFQRLQKLIPRHPGLYVP 122
Y L+EP+I D ++ LQ+L +HP L P
Sbjct: 12 YYVLDEPSISDAEYDRLYRELQELEEKHPELITP 45
>gnl|CDD|179086 PRK00683, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 418
Score = 26.7 bits (59), Expect = 3.9
Identities = 7/29 (24%), Positives = 14/29 (48%)
Query: 56 TSHAIRVQTPPRHIPGVVEVTLSYKSKQF 84
H HIP V ++ L++++ +F
Sbjct: 71 KEHPWVQAAIASHIPVVTDIQLAFQTPEF 99
>gnl|CDD|238062 cd00114, LIGANc, NAD+ dependent DNA ligase adenylation domain. DNA
ligases catalyze the crucial step of joining the breaks
in duplex DNA during DNA replication, repair and
recombination, utilizing either ATP or NAD(+) as a
cofactor, but using the same basic reaction mechanism.
The enzyme reacts with the cofactor to form a
phosphoamide-linked AMP with the amino group of a
conserved Lysine in the KXDG motif, and subsequently
transfers it to the DNA substrate to yield adenylated
DNA. This alignment contains members of the NAD+
dependent subfamily only.
Length = 307
Score = 26.4 bits (59), Expect = 3.9
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 6/34 (17%)
Query: 94 YVSLNEPTI-----DYGFQRLQKLIPRHPGLYVP 122
YV L+EP++ D ++ L+ L HP L P
Sbjct: 18 YV-LDEPSVSDAEYDRLYRELRALEEEHPELKTP 50
>gnl|CDD|213308 cd05943, AACS, Acetoacetyl-CoA synthetase (acetoacetate-CoA ligase,
AACS). AACS is a cytosolic ligase that specifically
activates acetoacetate to its coenzyme A ester by a
two-step reaction. Acetoacetate first reacts with ATP to
form an acyl-adenylate intermediate, which then reacts
with CoA to produce an acyl-CoA ester. This is the first
step of the mevalonate pathway of isoprenoid
biosynthesis via isopentenyl diphosphate. Isoprenoids
are a large class of compounds found in all living
organisms. AACS is widely distributed in bacteria,
archaea and eukaryotes. In bacteria, AACS is known to
exhibit an important role in the metabolism of
poly-b-hydroxybutyrate, an intracellular reserve of
organic carbon and chemical energy by some
microorganisms. In mammals, AACS influences the rate of
ketone body utilization for the formation of
physiologically important fatty acids and cholesterol.
Length = 616
Score = 26.4 bits (59), Expect = 4.3
Identities = 19/57 (33%), Positives = 24/57 (42%), Gaps = 11/57 (19%)
Query: 59 AIRVQTPPRHIPG-VVEV-----TLSYKS-----KQFCKGAPGRFVYVSLNEPTIDY 104
AIR PRH+P ++ V TLS K K+ G P V N +DY
Sbjct: 559 AIRAALSPRHVPAEIIAVPDIPYTLSGKKVEVAVKKILLGKPVENVAALANPECLDY 615
>gnl|CDD|223350 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type
II) [DNA replication, recombination, and repair].
Length = 667
Score = 26.4 bits (59), Expect = 4.7
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 6/34 (17%)
Query: 94 YVSLNEPTI-----DYGFQRLQKLIPRHPGLYVP 122
YV L+ P++ D ++ LQ+L +HP L P
Sbjct: 26 YV-LDAPSVSDAEYDQLYRELQELEEKHPELITP 58
>gnl|CDD|235134 PRK03584, PRK03584, acetoacetyl-CoA synthetase; Provisional.
Length = 655
Score = 26.3 bits (59), Expect = 5.5
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 6/28 (21%)
Query: 59 AIRVQTPPRHIPG-VVEV-----TLSYK 80
IR PRH+P ++ V TLS K
Sbjct: 586 TIRTNLSPRHVPDKIIAVPDIPRTLSGK 613
>gnl|CDD|182128 PRK09875, PRK09875, putative hydrolase; Provisional.
Length = 292
Score = 25.9 bits (57), Expect = 5.7
Identities = 12/43 (27%), Positives = 19/43 (44%)
Query: 18 PDEKSAFIPVTRASSPTSTPNSHFINANTSGWNHCTLITSHAI 60
P E+ FI A + T P S + +T G L+ +H +
Sbjct: 135 PLEEKVFIAAALAHNQTGRPISTHTSFSTMGLEQLALLQAHGV 177
>gnl|CDD|227217 COG4880, COG4880, Secreted protein containing C-terminal
beta-propeller domain distantly related to WD-40 repeats
[General function prediction only].
Length = 603
Score = 26.0 bits (57), Expect = 6.5
Identities = 8/18 (44%), Positives = 11/18 (61%)
Query: 9 YDHHTLSSDPDEKSAFIP 26
YDHH DP+ + F+P
Sbjct: 525 YDHHAFLYDPEAEIFFLP 542
>gnl|CDD|235534 PRK05618, PRK05618, 50S ribosomal protein L25/general stress
protein Ctc; Reviewed.
Length = 197
Score = 25.5 bits (57), Expect = 7.0
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 58 HAIRVQTPPRHIPGVVEVTLS 78
H + V+ P IP +EV +S
Sbjct: 130 HELEVECLPEDIPEFIEVDVS 150
>gnl|CDD|234978 PRK01747, mnmC, bifunctional tRNA
(mnm(5)s(2)U34)-methyltransferase/FAD-dependent
cmnm(5)s(2)U34 oxidoreductase; Reviewed.
Length = 662
Score = 26.0 bits (58), Expect = 7.3
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 107 QRLQKLIPRHPGLYV 121
Q+ + PR PGLYV
Sbjct: 593 QQPARDAPRLPGLYV 607
>gnl|CDD|165774 PLN00209, PLN00209, ribosomal protein S27; Provisional.
Length = 86
Score = 24.8 bits (54), Expect = 7.7
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 36 TPNSHFINANTSGWNHCTLITSHAIRV 62
+PNS F++ G + T + SH+ V
Sbjct: 29 SPNSFFMDVKCQGCFNITTVFSHSQTV 55
>gnl|CDD|114278 pfam05547, Peptidase_M6, Immune inhibitor A peptidase M6. The
insect pathogenic Gram-positive Bacillus thuringiensis
secretes immune inhibitor A, a metallopeptidase, which
specifically cleaves host antibacterial proteins. A
homologue of immune inhibitor A, PrtV, has been
identified in the Gram-negative human pathogen Vibrio
cholerae.
Length = 646
Score = 25.6 bits (56), Expect = 8.6
Identities = 14/27 (51%), Positives = 16/27 (59%)
Query: 70 PGVVEVTLSYKSKQFCKGAPGRFVYVS 96
PGVV+VTL KS + K A G Y S
Sbjct: 321 PGVVKVTLPKKSVEIIKPAEGETQYYS 347
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 0.133 0.417
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,157,783
Number of extensions: 493810
Number of successful extensions: 447
Number of sequences better than 10.0: 1
Number of HSP's gapped: 447
Number of HSP's successfully gapped: 27
Length of query: 123
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 38
Effective length of database: 7,167,512
Effective search space: 272365456
Effective search space used: 272365456
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: 53 (24.1 bits)