RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2712
(602 letters)
>gnl|CDD|240433 PTZ00482, PTZ00482, membrane-attack complex/perforin (MACPF)
Superfamily; Provisional.
Length = 844
Score = 41.0 bits (96), Expect = 0.002
Identities = 27/137 (19%), Positives = 52/137 (37%), Gaps = 6/137 (4%)
Query: 468 EPLLTQPSDSFSSLFFKEMIDQMKNCKDALNPDDENTNNVSALDLNGDENTNNVSALDLN 527
+ L D F L+ + D + DD++ + D + D NN D +
Sbjct: 84 KSLDDDDDDEFDFLYEDDEDDAGNATSGESSTDDDSLLELPDRDEDADTQANNDQTNDFD 143
Query: 528 GDENTNNVSALDLNGDENTNNVSALDLNGDEN--TNNVSALDLNGDENTNNVSALDLNGD 585
D+++N S D ++ N SA L ++ T N G++ +A G
Sbjct: 144 QDDSSN--SQTDQGLKQSVNLSSAEKLIEEKKGQTENTFKFYNFGNDGEE--AAAKDGGK 199
Query: 586 ENTNNVSALDLNGDESD 602
+++ L+ + + D
Sbjct: 200 SKSSDPGPLNDSDGQGD 216
>gnl|CDD|227614 COG5295, Hia, Autotransporter adhesin [Intracellular trafficking
and secretion / Extracellular structures].
Length = 715
Score = 38.3 bits (89), Expect = 0.012
Identities = 27/106 (25%), Positives = 35/106 (33%), Gaps = 14/106 (13%)
Query: 503 NTNNVSALDLNGDENTNNVSALDLN----GDENTNNVSALDLNGDENTNNVSALDLNGDE 558
T + A N D SAL+ G E T AL+ D D
Sbjct: 21 GTLSTVASGANVDAKGVGASALNAKALGGGKEVTALGGALNSGAVSLGTLSVVGDGGKDG 80
Query: 559 NTNNVSALDLNGD----------ENTNNVSALDLNGDENTNNVSAL 594
+TN ++L L D E NV+A N D VS +
Sbjct: 81 STNGDNSLGLTQDTGAAVSASKGEVITNVAAGLKNVDTMNVIVSII 126
Score = 37.2 bits (86), Expect = 0.027
Identities = 18/98 (18%), Positives = 28/98 (28%), Gaps = 4/98 (4%)
Query: 498 NPDDENTNNVSALDLNGDENTNNVSALDLNGDENTNNVSALDLNGD--ENTNNVSALDLN 555
E NV+A N D VS + LN + S+ G L+
Sbjct: 100 ASKGEVITNVAAGLKNVDTMNVIVSII-LNSGTGAASASSTLAAGTTIRAVATGKTAVLS 158
Query: 556 GDENTNNVSALDLNGDENTNNVSALDLNGDENTNNVSA 593
+ + V A + N + G N +
Sbjct: 159 TA-SASGVQAKATDSALGFENTAVDQQAGAAGLGNAAE 195
Score = 34.8 bits (80), Expect = 0.13
Identities = 22/105 (20%), Positives = 29/105 (27%), Gaps = 7/105 (6%)
Query: 500 DDENTNNVSALDLNGDENTNNVSALDLNGDENTNNVSALDLNGDENT--NNVSALDLNGD 557
N V + G S T +A NG NV + D
Sbjct: 541 SSTNAAGVDIVA-AGKNINGANSVALGGNGPATAVGAAAVANGSVAGDAVNVGVGSVGKD 599
Query: 558 ENTNNVSALDLNGDENTNNVSALDLNGDENTNNVSALDLNGDESD 602
NV+A D NVS LN + N + + D
Sbjct: 600 RQITNVAAGVTGTDA--VNVSQ--LNYTDQANTELNGKIGKVDRD 640
Score = 32.2 bits (73), Expect = 0.91
Identities = 28/113 (24%), Positives = 37/113 (32%), Gaps = 18/113 (15%)
Query: 503 NTNNVSALDLNGDENTNNVSALDLNGDENTNNVSALDLN------GDENTNNVSALDLNG 556
NT + + + T + A N D V A LN G E T AL+
Sbjct: 7 NTTGSTGIGTDAAAGTLSTVASGANVD--AKGVGASALNAKALGGGKEVTALGGALNSGA 64
Query: 557 DENTNNVSALDLNGDENTNNVSALDLNGD----------ENTNNVSALDLNGD 599
D D +TN ++L L D E NV+A N D
Sbjct: 65 VSLGTLSVVGDGGKDGSTNGDNSLGLTQDTGAAVSASKGEVITNVAAGLKNVD 117
Score = 29.1 bits (65), Expect = 8.6
Identities = 22/90 (24%), Positives = 30/90 (33%), Gaps = 8/90 (8%)
Query: 517 NTNNVSALDLNGDENTNNVSALDLNGDENTNNVSALDLN------GDENTNNVSALDLNG 570
NT + + + T + A N D V A LN G E T AL+
Sbjct: 7 NTTGSTGIGTDAAAGTLSTVASGANVD--AKGVGASALNAKALGGGKEVTALGGALNSGA 64
Query: 571 DENTNNVSALDLNGDENTNNVSALDLNGDE 600
D D +TN ++L L D
Sbjct: 65 VSLGTLSVVGDGGKDGSTNGDNSLGLTQDT 94
>gnl|CDD|222190 pfam13517, VCBS, Family description. This domain of about 100
residues is found in multiple (up to 35) copies in long
proteins from several species of Vibrio, Colwellia,
Bradyrhizobium, and Shewanella (hence the name VCBS) and
in smaller copy numbers in proteins from several other
bacteria. The large protein size and repeat copy
numbers, species distribution, and suggested activities
of several member proteins suggests a role for this
domain in adhesion (TIGR).
Length = 61
Score = 33.0 bits (76), Expect = 0.032
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 7/54 (12%)
Query: 511 DLNGDE-------NTNNVSALDLNGDENTNNVSALDLNGDENTNNVSALDLNGD 557
DL+GD + V NGD V++ L +V+ DL+GD
Sbjct: 1 DLDGDGRLDLVVASDGGVRLYLNNGDGTFTFVTSTLLGTGGGGTSVAVADLDGD 54
Score = 33.0 bits (76), Expect = 0.032
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 7/54 (12%)
Query: 525 DLNGDE-------NTNNVSALDLNGDENTNNVSALDLNGDENTNNVSALDLNGD 571
DL+GD + V NGD V++ L +V+ DL+GD
Sbjct: 1 DLDGDGRLDLVVASDGGVRLYLNNGDGTFTFVTSTLLGTGGGGTSVAVADLDGD 54
Score = 33.0 bits (76), Expect = 0.032
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 7/54 (12%)
Query: 539 DLNGDE-------NTNNVSALDLNGDENTNNVSALDLNGDENTNNVSALDLNGD 585
DL+GD + V NGD V++ L +V+ DL+GD
Sbjct: 1 DLDGDGRLDLVVASDGGVRLYLNNGDGTFTFVTSTLLGTGGGGTSVAVADLDGD 54
Score = 33.0 bits (76), Expect = 0.032
Identities = 15/54 (27%), Positives = 22/54 (40%), Gaps = 7/54 (12%)
Query: 553 DLNGDE-------NTNNVSALDLNGDENTNNVSALDLNGDENTNNVSALDLNGD 599
DL+GD + V NGD V++ L +V+ DL+GD
Sbjct: 1 DLDGDGRLDLVVASDGGVRLYLNNGDGTFTFVTSTLLGTGGGGTSVAVADLDGD 54
Score = 29.1 bits (66), Expect = 0.85
Identities = 11/41 (26%), Positives = 17/41 (41%)
Query: 503 NTNNVSALDLNGDENTNNVSALDLNGDENTNNVSALDLNGD 543
+ V NGD V++ L +V+ DL+GD
Sbjct: 14 SDGGVRLYLNNGDGTFTFVTSTLLGTGGGGTSVAVADLDGD 54
>gnl|CDD|238654 cd01344, PL2_Passenger_AT, Pertactin-like passenger domains
(virulence factors), C-terminal, subgroup 2, of
autotransporter proteins of the type V secretion system
of Gram-negative bacteria. This subgroup includes the
passenger domains of the nonprotease autotransporters,
Ag43, AIDA-1 and IcsA, as well as, the less
characterized ShdA, MisL, and BapA autotransporters.
Length = 188
Score = 35.0 bits (81), Expect = 0.056
Identities = 23/103 (22%), Positives = 31/103 (30%), Gaps = 7/103 (6%)
Query: 503 NTNNVSALDLNGDENTNNVSA-LDLNGDENTNNVSALDLNGDENTNNVSALDLNGDENTN 561
N DL ++ L L G T L L+ N LN N
Sbjct: 6 NGGWKLGGDLTLGGGALTLTTSLTLTGTLLTGGAGTLTLDSTSTWNITGTSTLNVG-NLT 64
Query: 562 NVSALDLNGDENTNNVSALDLNGDENTNN-VSALD--LNGDES 601
N +DL L + G+ N L+ L D+S
Sbjct: 65 NAGTIDLGNGSPAGGT--LTITGNYTGNGGTLRLNTVLGDDDS 105
Score = 28.4 bits (64), Expect = 8.6
Identities = 20/96 (20%), Positives = 29/96 (30%), Gaps = 6/96 (6%)
Query: 495 DALNPDDENTNNVSALDLNGDENTNNVSALDLNGDENTNNVSALDLNGDENTNNVSALDL 554
L ++L L G T L L+ N LN N N +DL
Sbjct: 13 GDLTLGGGALTLTTSLTLTGTLLTGGAGTLTLDSTSTWNITGTSTLNVG-NLTNAGTIDL 71
Query: 555 NGDENTNNVSALDLNGDENTNN-VSALD--LNGDEN 587
L + G+ N L+ L D++
Sbjct: 72 GNGSPAGGT--LTITGNYTGNGGTLRLNTVLGDDDS 105
>gnl|CDD|113681 pfam04917, Shufflon_N, Bacterial shufflon protein, N-terminal
constant region. This family represents the
high-similarity N-terminal 'constant region' shared by
shufflon proteins.
Length = 356
Score = 33.8 bits (77), Expect = 0.27
Identities = 21/83 (25%), Positives = 41/83 (49%), Gaps = 2/83 (2%)
Query: 495 DALNPDDENTNNVSALDLNGDENTNNV-SALDLNGDENTNNVSALDLNGDENTNNVSALD 553
D L+ E+++ + +NG + N + +A+D+ + N NNV ++ N + NVS +
Sbjct: 184 DDLSGAREDSDRLYRFQVNGRPDLNKMHTAIDMGSN-NLNNVGTVNANAAALSGNVSGRN 242
Query: 554 LNGDENTNNVSALDLNGDENTNN 576
+ +A+ GD +NN
Sbjct: 243 GTFSGAISGNTAITAGGDIRSNN 265
Score = 33.0 bits (75), Expect = 0.37
Identities = 28/115 (24%), Positives = 52/115 (45%), Gaps = 9/115 (7%)
Query: 484 KEMIDQMKNCKDALNPDDENTNN------VSALDLNG-DENTNNVSALDLNGDENTNNV- 535
K I ++ D L+ N +S DL+G E+++ + +NG + N +
Sbjct: 152 KTAIGAGRSWSDTLSNYGLNCGTGHIAVALSTDDLSGAREDSDRLYRFQVNGRPDLNKMH 211
Query: 536 SALDLNGDENTNNVSALDLNGDENTNNVSALDLNGDENTNNVSALDLNGDENTNN 590
+A+D+ + N NNV ++ N + NVS + + +A+ GD +NN
Sbjct: 212 TAIDMGSN-NLNNVGTVNANAAALSGNVSGRNGTFSGAISGNTAITAGGDIRSNN 265
Score = 30.0 bits (67), Expect = 3.4
Identities = 21/81 (25%), Positives = 41/81 (50%), Gaps = 3/81 (3%)
Query: 521 VSALDLNG-DENTNNVSALDLNGDENTNNV-SALDLNGDENTNNVSALDLNGDENTNNVS 578
+S DL+G E+++ + +NG + N + +A+D+ + N NNV ++ N + NVS
Sbjct: 181 LSTDDLSGAREDSDRLYRFQVNGRPDLNKMHTAIDMGSN-NLNNVGTVNANAAALSGNVS 239
Query: 579 ALDLNGDENTNNVSALDLNGD 599
+ + +A+ GD
Sbjct: 240 GRNGTFSGAISGNTAITAGGD 260
>gnl|CDD|224176 COG1256, FlgK, Flagellar hook-associated protein [Cell motility and
secretion].
Length = 552
Score = 32.0 bits (73), Expect = 1.1
Identities = 22/94 (23%), Positives = 37/94 (39%), Gaps = 5/94 (5%)
Query: 511 DLNGDENTNNVSALDLNGDENTNNVSALDLNGDENTNNVSA----LDLNGDENTNNVSAL 566
+L NT AL + N + + LDLNG E + + + L D++ N+S+
Sbjct: 291 ELAPTLNTLGQLALSFLDEFNKGHGAGLDLNGAEGADFFNIEGLPVILTNDKSNGNISSG 350
Query: 567 DLN-GDENTNNVSALDLNGDENTNNVSALDLNGD 599
D N + + + GD + L N
Sbjct: 351 GFTVSDANKVGATTIPVTGDVVPGIATRLSDNVT 384
Score = 30.1 bits (68), Expect = 4.0
Identities = 24/108 (22%), Positives = 42/108 (38%), Gaps = 5/108 (4%)
Query: 498 NPDDENTNNVSALD---LNGDENTNNVSALDLNGDENTNNVSALDLNGDENTNNVSALDL 554
+ ++ N++ + L + L + DE NV +D DE N++
Sbjct: 219 SKREDGDYNLTTGNGTTLVEGSEAKVFAPLPGSDDETRGNVIYVD-GDDEKAGNITNTLS 277
Query: 555 NGD-ENTNNVSALDLNGDENTNNVSALDLNGDENTNNVSALDLNGDES 601
G ++ + +L NT AL + N + + LDLNG E
Sbjct: 278 GGKLGGLLDLRSDELAPTLNTLGQLALSFLDEFNKGHGAGLDLNGAEG 325
>gnl|CDD|239571 cd03489, Topoisomer_IB_N_LdtopoI_like,
Topoisomer_IB_N_LdtopoI_like: N-terminal DNA binding
fragment found in eukaryotic DNA topoisomerase (topo) IB
proteins similar to the heterodimeric topo I from
Leishmania donvanni. Topo I enzymes are divided into:
topo type IA (bacterial) and type IB (eukaryotic). Topo
I relaxes superhelical tension in duplex DNA by creating
a single-strand nick, the broken strand can then rotate
around the unbroken strand to remove DNA supercoils and,
the nick is religated, liberating topo I. These enzymes
regulate the topological changes that accompany DNA
replication, transcription and other nuclear processes.
Human topo I is the target of a diverse set of
anticancer drugs including camptothecins (CPTs). CPTs
bind to the topo I-DNA complex and inhibit re-ligation
of the single-strand nick, resulting in the accumulation
of topo I-DNA adducts. In addition to differences in
structure and some biochemical properties,
Trypanosomatid parasite topo I differ from human topo I
in their sensitivity to CPTs and other classical topo I
inhibitors. Trypanosomatid topo I play putative roles in
organizing the kinetoplast DNA network unique to these
parasites. This family may represent more than one
structural domain.
Length = 212
Score = 28.7 bits (64), Expect = 7.4
Identities = 17/57 (29%), Positives = 23/57 (40%), Gaps = 4/57 (7%)
Query: 372 PEVREIFANKLHKGLGRN-LPNKCLPL-DFMGFYALGGLEEEKKLKMSTE--KALAQ 424
R F + L + P + L L DF Y E+EKK + E KAL +
Sbjct: 55 EVFRRNFFESWREILDKRHHPIRKLELCDFTPIYEWHLREKEKKKSRTKEEKKALKE 111
>gnl|CDD|224763 COG1850, RbcL, Ribulose 1,5-bisphosphate carboxylase, large subunit
[Carbohydrate transport and metabolism].
Length = 429
Score = 29.2 bits (66), Expect = 7.4
Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 11/62 (17%)
Query: 215 PDSPNYRTAIIALGHIAY--------NMPNKFPAVIKNTVSRKIVKELLIKETEESYQYK 266
P + AI+ IAY ++P +V N K +K L +++ ++
Sbjct: 77 PGEDGQKRAIV---KIAYPLDLFEEGSLPALLTSVAGNVFGMKALKGLRLEDLRFPKEFL 133
Query: 267 KD 268
K
Sbjct: 134 KA 135
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
0.316 0.134 0.384
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 30,446,312
Number of extensions: 3025456
Number of successful extensions: 2628
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2603
Number of HSP's successfully gapped: 35
Length of query: 602
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 500
Effective length of database: 6,413,494
Effective search space: 3206747000
Effective search space used: 3206747000
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 (21.6 bits)
S2: 62 (27.7 bits)