RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5107
(74 letters)
>gnl|CDD|238684 cd01388, SOX-TCF_HMG-box, SOX-TCF_HMG-box, class I member of the
HMG-box superfamily of DNA-binding proteins. These
proteins contain a single HMG box, and bind the minor
groove of DNA in a highly sequence-specific manner.
Members include SRY and its homologs in insects and
vertebrates, and transcription factor-like proteins,
TCF-1, -3, -4, and LEF-1. They appear to bind the minor
groove of the A/T C A A A G/C-motif.
Length = 72
Score = 56.5 bits (137), Expect = 9e-13
Identities = 20/37 (54%), Positives = 25/37 (67%)
Query: 17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
HIKRPMNAFM++S+ RRK+ + P N ISK L
Sbjct: 1 HIKRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILG 37
>gnl|CDD|189580 pfam00505, HMG_box, HMG (high mobility group) box.
Length = 69
Score = 48.8 bits (117), Expect = 1e-09
Identities = 17/36 (47%), Positives = 24/36 (66%)
Query: 18 IKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
KRP++AF ++SQ +R K+ P + NAEISK L
Sbjct: 1 PKRPLSAFFLFSQEQRAKLKAENPGLKNAEISKILG 36
>gnl|CDD|197700 smart00398, HMG, high mobility group.
Length = 70
Score = 48.5 bits (116), Expect = 1e-09
Identities = 21/37 (56%), Positives = 26/37 (70%)
Query: 17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
KRPM+AFM++SQ R KI PD+ NAEISK+L
Sbjct: 1 KPKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLG 37
>gnl|CDD|238037 cd00084, HMG-box, High Mobility Group (HMG)-box is found in a
variety of eukaryotic chromosomal proteins and
transcription factors. HMGs bind to the minor groove of
DNA and have been classified by DNA binding
preferences. Two phylogenically distinct groups of
Class I proteins bind DNA in a sequence specific
fashion and contain a single HMG box. One group
(SOX-TCF) includes transcription factors, TCF-1, -3,
-4; and also SRY and LEF-1, which bind four-way DNA
junctions and duplex DNA targets. The second group
(MATA) includes fungal mating type gene products MC,
MATA1 and Ste11. Class II and III proteins (HMGB-UBF)
bind DNA in a non-sequence specific fashion and contain
two or more tandem HMG boxes. Class II members include
non-histone chromosomal proteins, HMG1 and HMG2, which
bind to bent or distorted DNA such as four-way DNA
junctions, synthetic DNA cruciforms, kinked
cisplatin-modified DNA, DNA bulges, cross-overs in
supercoiled DNA, and can cause looping of linear DNA.
Class III members include nucleolar and mitochondrial
transcription factors, UBF and mtTF1, which bind
four-way DNA junctions.
Length = 66
Score = 47.2 bits (113), Expect = 4e-09
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 18 IKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
KRP++A+ ++SQ R ++ P + EISK L
Sbjct: 1 PKRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILG 36
>gnl|CDD|238686 cd01390, HMGB-UBF_HMG-box, HMGB-UBF_HMG-box, class II and III
members of the HMG-box superfamily of DNA-binding
proteins. These proteins bind the minor groove of DNA
in a non-sequence specific fashion and contain two or
more tandem HMG boxes. Class II members include
non-histone chromosomal proteins, HMG1 and HMG2, which
bind to bent or distorted DNA such as four-way DNA
junctions, synthetic DNA cruciforms, kinked
cisplatin-modified DNA, DNA bulges, cross-overs in
supercoiled DNA, and can cause looping of linear DNA.
Class III members include nucleolar and mitochondrial
transcription factors, UBF and mtTF1, which bind
four-way DNA junctions.
Length = 66
Score = 39.1 bits (92), Expect = 6e-06
Identities = 13/35 (37%), Positives = 23/35 (65%)
Query: 19 KRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
KRP++A+ ++SQ +R K+ + PD E++K L
Sbjct: 2 KRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILG 36
>gnl|CDD|227935 COG5648, NHP6B, Chromatin-associated proteins containing the HMG
domain [Chromatin structure and dynamics].
Length = 211
Score = 39.1 bits (91), Expect = 4e-05
Identities = 16/49 (32%), Positives = 27/49 (55%)
Query: 5 SPMRATKKNNPNHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
S KK +PN KRP++A+ ++S R +I + P + E+ K L+
Sbjct: 58 SKRLVRKKKDPNGPKRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLS 106
>gnl|CDD|238685 cd01389, MATA_HMG-box, MATA_HMG-box, class I member of the
HMG-box superfamily of DNA-binding proteins. These
proteins contain a single HMG box, and bind the minor
groove of DNA in a highly sequence-specific manner.
Members include the fungal mating type gene products
MC, MATA1 and Ste11.
Length = 77
Score = 35.3 bits (82), Expect = 2e-04
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 17 HIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLA 53
I RP NAF+++ Q + ++ P + N EIS+ +
Sbjct: 1 KIPRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIG 37
>gnl|CDD|185511 PTZ00199, PTZ00199, high mobility group protein; Provisional.
Length = 94
Score = 26.7 bits (59), Expect = 0.70
Identities = 11/33 (33%), Positives = 22/33 (66%)
Query: 11 KKNNPNHIKRPMNAFMVWSQMERRKICEVQPDM 43
KK +PN KR ++A+M +++ +R +I P++
Sbjct: 16 KKKDPNAPKRALSAYMFFAKEKRAEIIAENPEL 48
>gnl|CDD|219171 pfam06776, IalB, Invasion associated locus B (IalB) protein.
This family consists of several invasion associated
locus B (IalB) proteins and related sequences. IalB is
known to be a major virulence factor in Bartonella
bacilliformis where it was shown to have a direct role
in human erythrocyte parasitism. IalB is upregulated in
response to environmental cues signaling vector-to-host
transmission. Such environmental cues would include,
but not be limited to, temperature, pH, oxidative
stress, and haemin limitation. It is also thought that
IalB would aide B. bacilliformis survival under
stress-inducing environmental conditions. The role of
this protein in other bacterial species is unknown.
Length = 133
Score = 26.1 bits (58), Expect = 1.4
Identities = 6/33 (18%), Positives = 15/33 (45%)
Query: 32 ERRKICEVQPDMHNAEISKRLALLSLYKSNGFN 64
E + +C + + + E + +A +SL +
Sbjct: 13 EAKDVCNLSQLLVDEETGQPVAAVSLIRLADGG 45
>gnl|CDD|240370 PTZ00342, PTZ00342, acyl-CoA synthetase; Provisional.
Length = 746
Score = 25.4 bits (56), Expect = 2.5
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 54 LLSLYKSNGFNWLLAE 69
LL LY SN NWL+A+
Sbjct: 132 LLGLYGSNSINWLVAD 147
>gnl|CDD|215289 PLN02528, PLN02528, 2-oxoisovalerate dehydrogenase E2 component.
Length = 416
Score = 25.1 bits (55), Expect = 3.9
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 32 ERRKICEVQPDMHNAEISKR 51
E + +CEVQ D EI+ R
Sbjct: 28 EFQPLCEVQSDKATIEITSR 47
>gnl|CDD|185657 PTZ00479, PTZ00479, RAP Superfamily; Provisional.
Length = 435
Score = 24.0 bits (52), Expect = 8.8
Identities = 11/50 (22%), Positives = 19/50 (38%)
Query: 16 NHIKRPMNAFMVWSQMERRKICEVQPDMHNAEISKRLALLSLYKSNGFNW 65
+ + + +F M R +P ++S LA L + N F W
Sbjct: 267 FQLSKSVKSFYTRLSMRRIPQSLRKPSPFQWDVSNCLAKLGISHRNTFYW 316
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
0.322 0.132 0.414
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,710,733
Number of extensions: 262773
Number of successful extensions: 186
Number of sequences better than 10.0: 1
Number of HSP's gapped: 186
Number of HSP's successfully gapped: 16
Length of query: 74
Length of database: 10,937,602
Length adjustment: 44
Effective length of query: 30
Effective length of database: 8,986,026
Effective search space: 269580780
Effective search space used: 269580780
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)