RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9275
(284 letters)
>gnl|CDD|218636 pfam05557, MAD, Mitotic checkpoint protein. This family consists
of several eukaryotic mitotic checkpoint (Mitotic arrest
deficient or MAD) proteins. The mitotic spindle
checkpoint monitors proper attachment of the bipolar
spindle to the kinetochores of aligned sister chromatids
and causes a cell cycle arrest in prometaphase when
failures occur. Multiple components of the mitotic
spindle checkpoint have been identified in yeast and
higher eukaryotes. In S.cerevisiae, the existence of a
Mad1-dependent complex containing Mad2, Mad3, Bub3 and
Cdc20 has been demonstrated.
Length = 722
Score = 95.8 bits (238), Expect = 3e-22
Identities = 71/217 (32%), Positives = 113/217 (52%), Gaps = 22/217 (10%)
Query: 77 RAKLEVLEKVIEGYRQRMEHIEADQGLVCVI----------------PGQNSEKVAQQKV 120
R K+E LE+ + RQ +E +C+ P +E++A+Q +
Sbjct: 509 RLKIETLERERDRLRQEKSLLEMKLEHLCLQGDYNASRTKVLHMSLNPASEAEQIAKQTI 568
Query: 121 QELQMEADNNRETVKQMAGMQKLNSKIKSLELQGKRLREVYKAAKLNNKIKSLELQGKRL 180
+ LQ E + +E ++ + S+ LE + A+L +++S E + +RL
Sbjct: 569 EALQAECEKLKERLQALEE---GKSQPGDLEKAVGSHISSKEIAQLKKQVESAEKKNQRL 625
Query: 181 REVYKAASQEFRETVYLLFGYKVD-RTNCMYKLASMYADGPDENLLFQSTE--GQLNLIE 237
+EV++ EFR Y+LFGYK+D N Y+L SMYA+ D+ L+F++ G + L+E
Sbjct: 626 KEVFQTKISEFRRACYMLFGYKIDITPNSQYRLTSMYAEHDDDKLIFKAESSNGSMQLLE 685
Query: 238 TDYSKVLKPLLDLHLGRHHSIPMLLSALTQELFQRQT 274
T S L++LHL + +SIP LSALT ELF RQT
Sbjct: 686 TPSSGTFAKLIELHLLKQNSIPAFLSALTLELFSRQT 722
>gnl|CDD|217817 pfam03961, DUF342, Protein of unknown function (DUF342). This
family of bacterial proteins has no known function. The
proteins are in the region of 500-600 amino acid
residues in length.
Length = 450
Score = 34.5 bits (80), Expect = 0.060
Identities = 21/113 (18%), Positives = 49/113 (43%), Gaps = 13/113 (11%)
Query: 59 ALKGNATFSESAAPPGSDRAKLEVLEKVIEGYRQRMEHIEADQGLVCVIPGQNSEKVAQQ 118
+ G T E + +L+ LE+ ++ + +E I+ +P + ++ +
Sbjct: 315 SPAGTKTEIEVGVDFPELKEELKELEEELKELEEELEKIKKLLKK---LPKKARGQLPPE 371
Query: 119 KVQELQMEADNNRETVKQMAGMQKLNSKIKSLELQGKRLREVYKAAKLNNKIK 171
K ++L+ K + +KL+ +++ LE + K L+E ++ KI
Sbjct: 372 KREQLE----------KLLETKEKLSEELEELEEELKELKEELESLYSEGKIS 414
>gnl|CDD|227355 COG5022, COG5022, Myosin heavy chain [Cytoskeleton].
Length = 1463
Score = 33.5 bits (77), Expect = 0.13
Identities = 29/177 (16%), Positives = 62/177 (35%), Gaps = 23/177 (12%)
Query: 3 WRALKALKGKSTLKVLVILVELGYLSSNRERERDELLREKELKEKVDHLTYQMEWRALKG 62
R+LKA K S LK I ++ ER+ EL + + + + ++E ++
Sbjct: 852 GRSLKAKKRFSLLKKETIYLQSAQRVELAERQLQELKIDVKSISSLKLVNLELESEIIEL 911
Query: 63 NATFSESAAPPGSDRAKLEVLEKVIEGYRQRMEHIEADQGLVCVIPGQNSEKVAQQKVQE 122
+ S LE ++I ++ + +I+ ++G E V ++ +
Sbjct: 912 KKSLSSDL------IENLEFKTELIARLKKLLNNIDLEEGPSI-------EYVKLPELNK 958
Query: 123 LQMEADNNRETVKQMAGMQKLNSKIKSLELQGKRLREVYKAAKLNNKIKSLELQGKR 179
L + +++ + + + L + L A K EL
Sbjct: 959 LHE----------VESKLKETSEEYEDLLKKSTILVREGNKANSELKNFKKELAELS 1005
>gnl|CDD|224117 COG1196, Smc, Chromosome segregation ATPases [Cell division and
chromosome partitioning].
Length = 1163
Score = 32.8 bits (75), Expect = 0.22
Identities = 35/164 (21%), Positives = 76/164 (46%), Gaps = 30/164 (18%)
Query: 32 ERERDELLREKELKEKVDHLTYQMEWRALKGNATFSESAAPPGSDRAKLEVLEKVIEGYR 91
ER+ ++ R +ELK ++ L + LK R +LE LE+ +
Sbjct: 206 ERQAEKAERYQELKAELRELELALLLAKLKEL-------------RKELEELEEELSRLE 252
Query: 92 QRMEHIEADQGLVCVIPGQNSEKVAQ--QKVQELQMEADNNRETVKQMAGMQKLNSKIKS 149
+ +E ++ + + +++ + +++EL+ E + +E + +L +I+
Sbjct: 253 EELEELQEEL-------EEAEKEIEELKSELEELREELEELQEEL------LELKEEIEE 299
Query: 150 LELQGKRLREVYKAAKLNNKIKSLELQGKRLREVYKAASQEFRE 193
LE + LRE + +L N+++ LE + + L+E +A +E E
Sbjct: 300 LEGEISLLRE--RLEELENELEELEERLEELKEKIEALKEELEE 341
>gnl|CDD|214661 smart00435, TOPEUc, DNA Topoisomerase I (eukaryota). DNA
Topoisomerase I (eukaryota), DNA topoisomerase V,
Vaccina virus topoisomerase, Variola virus
topoisomerase, Shope fibroma virus topoisomeras.
Length = 391
Score = 31.9 bits (73), Expect = 0.36
Identities = 19/63 (30%), Positives = 37/63 (58%), Gaps = 3/63 (4%)
Query: 129 NNRETVKQM--AGMQKLNSKIKSLELQGKRLREVYKAAKLNNKIKSLELQGKRLREVYKA 186
N++ TV + M+KL KIK+L+ Q KRL+++ ++ + +K +L+ K R+ K
Sbjct: 266 NHQRTVSKTHEKSMEKLQEKIKALKYQLKRLKKMILLFEMISDLKR-KLKSKFERDNEKL 324
Query: 187 ASQ 189
++
Sbjct: 325 DAE 327
>gnl|CDD|237057 PRK12323, PRK12323, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 700
Score = 31.8 bits (72), Expect = 0.43
Identities = 17/94 (18%), Positives = 33/94 (35%), Gaps = 8/94 (8%)
Query: 37 ELLREKELKEKVDHLTYQMEWRALKGNATFSESAAPPGSDRAKLEVLEKVIEGYRQRMEH 96
L ++ L Q E ++G+ P ++ +E L+ + EH
Sbjct: 583 ALAARLPVRGLAQQLARQSELAGVEGDTVRLRVPVPALAEAEVVERLQAAL------TEH 636
Query: 97 IEADQGLVCVI--PGQNSEKVAQQKVQELQMEAD 128
+VC + G + V ++ E Q A+
Sbjct: 637 FGQPVRVVCEVGAVGATAAAVDAEERAERQRAAE 670
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 31.2 bits (71), Expect = 0.68
Identities = 18/106 (16%), Positives = 39/106 (36%), Gaps = 1/106 (0%)
Query: 83 LEKVIEGYRQRMEHIEADQGLVCVIPGQNSEKVAQQKVQELQMEADNNRETVKQMAGMQK 142
+ +R++ ++A + + + + + A+ + A + +
Sbjct: 152 YGALNPARAERIDALKATLKQLAAVRAEIAAEQAELTTLLSEQRAQQAKLAQLLEERKKT 211
Query: 143 LNSKIKSLELQGKRLREV-YKAAKLNNKIKSLELQGKRLREVYKAA 187
L L K+L E+ ++L N+I S E + RE AA
Sbjct: 212 LAQLNSELSADQKKLEELRANESRLKNEIASAEAAAAKAREAAAAA 257
>gnl|CDD|220329 pfam09657, Cas_Csx8, CRISPR-associated protein Csx8 (Cas_Csx8).
Clusters of short DNA repeats with nonhomologous
spacers, which are found at regular intervals in the
genomes of phylogenetically distinct prokaryotic
species, comprise a family with recognisable features.
This family is known as CRISPR (short for Clustered,
Regularly Interspaced Short Palindromic Repeats). A
number of protein families appear only in association
with these repeats and are designated Cas
(CRISPR-Associated) proteins. This entry describes
proteins of unknown function which are encoded in the
midst of a cas gene operon.
Length = 441
Score = 31.0 bits (70), Expect = 0.72
Identities = 12/69 (17%), Positives = 28/69 (40%)
Query: 129 NNRETVKQMAGMQKLNSKIKSLELQGKRLREVYKAAKLNNKIKSLELQGKRLREVYKAAS 188
N+ ++ + K + K+ E +G + + N + ++ + + K
Sbjct: 208 NDNLDIEILKKSNKAIKEKKNEETEGNQNSVPLRKTLFNILQEKVDYIKYDVEVILKNRD 267
Query: 189 QEFRETVYL 197
+E+ ET YL
Sbjct: 268 KEYFETWYL 276
>gnl|CDD|187875 cd09744, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Large proteins, some contain Zn-finger domain; signature
gene for I-A subtype; also known as Csx8 family.
Length = 441
Score = 31.0 bits (70), Expect = 0.72
Identities = 12/69 (17%), Positives = 28/69 (40%)
Query: 129 NNRETVKQMAGMQKLNSKIKSLELQGKRLREVYKAAKLNNKIKSLELQGKRLREVYKAAS 188
N+ ++ + K + K+ E +G + + N + ++ + + K
Sbjct: 208 NDNLDIEILKKSNKAIKEKKNEETEGNQNSVPLRKTLFNILQEKVDYIKYDVEVILKNRD 267
Query: 189 QEFRETVYL 197
+E+ ET YL
Sbjct: 268 KEYFETWYL 276
>gnl|CDD|187828 cd09697, Cas8a1_I-A, CRISPR/Cas system-associated protein Cas8a1.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Large proteins, some contain Zn-finger domain; signature
gene for I-A subtype; also known as Csx8 family.
Length = 441
Score = 30.6 bits (69), Expect = 0.84
Identities = 12/69 (17%), Positives = 28/69 (40%)
Query: 129 NNRETVKQMAGMQKLNSKIKSLELQGKRLREVYKAAKLNNKIKSLELQGKRLREVYKAAS 188
N+ ++ + K + K+ E +G+ + N + ++ + + K
Sbjct: 208 NDNLDIEILKKSNKAIKEKKNEETEGENNSVPLRKTLFNILQEKVDYIKYDVEVILKNRD 267
Query: 189 QEFRETVYL 197
+E+ ET YL
Sbjct: 268 KEYFETWYL 276
>gnl|CDD|233970 TIGR02670, cas_csx8, CRISPR-associated protein Cas8a1/Csx8, subtype
I. In three genomes so far, a member of this protein
appears in the midst of a CRISPR-associated (cas) gene
operon, immediately upstream of a member of family
TIGR01875 (CRISPR-associated autoregulator, DevR
family). The genomes so far are Nocardia farcinica
IFM10152, Clostridium perfringens SM101, and Clostridium
tetani E88 [Mobile and extrachromosomal element
functions, Other].
Length = 441
Score = 30.6 bits (69), Expect = 0.84
Identities = 12/69 (17%), Positives = 28/69 (40%)
Query: 129 NNRETVKQMAGMQKLNSKIKSLELQGKRLREVYKAAKLNNKIKSLELQGKRLREVYKAAS 188
N+ ++ + K + K+ E +G+ + N + ++ + + K
Sbjct: 208 NDNLDIEILKKSNKAIKEKKNEETEGENNSVPLRKTLFNILQEKVDYIKYDVEVILKNRD 267
Query: 189 QEFRETVYL 197
+E+ ET YL
Sbjct: 268 KEYFETWYL 276
>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 = 30.8 bits (70), Expect = 0.97
Identities = 29/173 (16%), Positives = 72/173 (41%), Gaps = 16/173 (9%)
Query: 30 NRERERDELLREK--ELKEKVDHLTYQMEWRALKGNATFSESAAPPGSDRAKLEVLEKVI 87
NR E L ++ EL+E+ L Q++ +LE LE +
Sbjct: 822 NRLTLEKEYLEKEIQELQEQRIDLKEQIKSIE----KEIENLNGKKEELEEELEELEAAL 877
Query: 88 EGYRQRMEHIEADQGLVCVIPGQNSEKVAQQKVQELQMEADNNRETVKQM-AGMQKLNSK 146
R+ ++ ++ + + + ++K++EL+ + + R+ + ++ A ++ L +
Sbjct: 878 RDLESRLGDLKKERDEL-----EAQLRELERKIEELEAQIEKKRKRLSELKAKLEALEEE 932
Query: 147 IKSLELQGKRLREVYKAA----KLNNKIKSLELQGKRLREVYKAASQEFRETV 195
+ +E E+ + + +++ +E + + L V A QE+ E +
Sbjct: 933 LSEIEDPKGEDEEIPEEELSLEDVQAELQRVEEEIRALEPVNMLAIQEYEEVL 985
Score = 28.5 bits (64), Expect = 5.8
Identities = 26/126 (20%), Positives = 52/126 (41%), Gaps = 17/126 (13%)
Query: 77 RAKLEVLEKVIEGYRQRMEHIEADQGLVCVIPGQNSEKVAQQKVQELQMEADNNRETVKQ 136
A++E LE+ IE R+R + + + ++ + EL+ ET +
Sbjct: 335 LAEIEELEREIEEERKRRDKLTEEY--------AELKEELEDLRAELEEVDKEFAETRDE 386
Query: 137 MAGMQK----LNSKIKSLELQGKRLREVYKA-----AKLNNKIKSLELQGKRLREVYKAA 187
+ ++ L +I L+ + RL+E + A LN I +E + L E +
Sbjct: 387 LKDYREKLEKLKREINELKRELDRLQEELQRLSEELADLNAAIAGIEAKINELEEEKEDK 446
Query: 188 SQEFRE 193
+ E ++
Sbjct: 447 ALEIKK 452
>gnl|CDD|189762 pfam00901, Orbi_VP5, Orbivirus outer capsid protein VP5.
cryoelectron microscopy indicates that VP5 is a trimer
implying that there are 360 copies of VP5 per virion.
Length = 507
Score = 30.4 bits (69), Expect = 1.1
Identities = 28/100 (28%), Positives = 44/100 (44%), Gaps = 28/100 (28%)
Query: 113 EKVAQQKVQELQMEADNNRETVKQMAGMQKLNSKIKSLELQGKRLREVYKAAKLNNKI-- 170
E+ Q+K++EL+ E E V++ K N KI +E G+ L EVYK K K+
Sbjct: 86 EQGLQRKLKELERE--QKEEEVRE-----KHNKKI--IEKFGEDLEEVYKFMKGEAKVEE 136
Query: 171 -----------------KSLELQGKRLREVYKAASQEFRE 193
K ++ + K L+ + KA +E E
Sbjct: 137 EEEKQMEILEKALKSYLKIVKEENKSLQRLAKALQKESEE 176
>gnl|CDD|224705 COG1792, MreC, Cell shape-determining protein [Cell envelope
biogenesis, outer membrane].
Length = 284
Score = 30.0 bits (68), Expect = 1.2
Identities = 14/42 (33%), Positives = 28/42 (66%)
Query: 118 QKVQELQMEADNNRETVKQMAGMQKLNSKIKSLELQGKRLRE 159
+ ++ L+ A N E K++A +++L +++SLE + KRL+E
Sbjct: 63 EFLKSLKDLALENEELKKELAELEQLLEEVESLEEENKRLKE 104
>gnl|CDD|227250 COG4913, COG4913, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 1104
Score = 30.0 bits (67), Expect = 1.7
Identities = 15/90 (16%), Positives = 34/90 (37%), Gaps = 10/90 (11%)
Query: 116 AQQKVQELQMEADNNRETVKQMAGMQKLNSKIKSL---------ELQGKRLREV-YKAAK 165
++++ L K N+ K+L E Q +R+ + +
Sbjct: 254 IKRQIHTLDPLVQLKNRREKAQQSKDHANALKKALPTVGNRIKKEEQETLVRQFTVEQTQ 313
Query: 166 LNNKIKSLELQGKRLREVYKAASQEFRETV 195
+K++S +++ R RE+ A ++ V
Sbjct: 314 AKSKVESAKIETDRAREMETLAHDNVKQIV 343
>gnl|CDD|233757 TIGR02168, SMC_prok_B, chromosome segregation protein SMC, common
bacterial 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. This family
represents the SMC protein of most bacteria. The smc
gene is often associated with scpB (TIGR00281) and scpA
genes, where scp stands for segregation and condensation
protein. SMC was shown (in Caulobacter crescentus) to be
induced early in S phase but present and bound to DNA
throughout the cell cycle [Cellular processes, Cell
division, DNA metabolism, Chromosome-associated
proteins].
Length = 1179
Score = 29.6 bits (67), Expect = 2.2
Identities = 33/189 (17%), Positives = 65/189 (34%), Gaps = 25/189 (13%)
Query: 22 VELGYLSSNRERERDELLREKELKEKVDHLTYQMEWRALKGNATFSESAAPPGSDRAKLE 81
E L E + + E ++ ++ A E ++LE
Sbjct: 817 EEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELESELE 876
Query: 82 VLEKVIEGYRQRMEHIEADQGLVCVIPGQNSEKVAQQKVQELQMEADNNRETVKQM-AGM 140
L + + + ++ + + + K EL+ E + RE + Q+ +
Sbjct: 877 ALLNERASLEEALALLRSELEEL-----SEELRELESKRSELRRELEELREKLAQLELRL 931
Query: 141 QKLNSKIKSLELQGKRLREVYK----------------AAKLNNKIKSLELQGKRLREVY 184
+ L +I +L+ +RL E Y + ++K LE + K L V
Sbjct: 932 EGLEVRIDNLQ---ERLSEEYSLTLEEAEALENKIEDDEEEARRRLKRLENKIKELGPVN 988
Query: 185 KAASQEFRE 193
AA +E+ E
Sbjct: 989 LAAIEEYEE 997
>gnl|CDD|225288 COG2433, COG2433, Uncharacterized conserved protein [Function
unknown].
Length = 652
Score = 29.3 bits (66), Expect = 2.7
Identities = 30/130 (23%), Positives = 59/130 (45%), Gaps = 11/130 (8%)
Query: 81 EVLEKVIEGYRQRMEHIEADQGLVCVIPGQNSEKVAQQKVQELQMEADNNRETVKQMAGM 140
E L KV E R R + ++ + + K ++ V+ L+ E N E +++ +
Sbjct: 392 EALSKVKEEERPREKEGTEEEERREITVYEKRIKKLEETVERLEEE---NSELKRELEEL 448
Query: 141 QKLNSKIKSLELQGKRLREVYKAAKLNNKIKSLE-----LQGKRLREVYKAASQEFRETV 195
++ K++S EL+ R REV + + +I++ + L+ K L E K + R+
Sbjct: 449 KREIEKLES-ELERFR-REVRDKVRKDREIRARDRRIERLE-KELEEKKKRVEELERKLA 505
Query: 196 YLLFGYKVDR 205
L K++
Sbjct: 506 ELRKMRKLEL 515
>gnl|CDD|235461 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 28.9 bits (66), Expect = 3.1
Identities = 15/71 (21%), Positives = 30/71 (42%), Gaps = 16/71 (22%)
Query: 114 KVAQQKVQELQME-----------ADNNRETVKQMAGMQKLNSKIKSLELQGKRLREVYK 162
+ Q +++ELQ E + +A +++L +IK+LE L E+
Sbjct: 38 RELQTELEELQAERNALSKEIGQAKRKGEDAEALIAEVKELKEEIKALE---AELDEL-- 92
Query: 163 AAKLNNKIKSL 173
A+L + +
Sbjct: 93 EAELEELLLRI 103
>gnl|CDD|185764 cd09241, BRO1_ScRim20-like, Protein-interacting, N-terminal,
Bro1-like domain of Saccharomyces cerevisiae Rim20 and
related proteins. This family contains the N-terminal,
Bro1-like domain of Saccharomyces cerevisiae Rim20 (also
known as PalA) and related proteins. It belongs to the
BRO1_Alix_like superfamily which also includes the
Bro1-like domains of mammalian Alix (apoptosis-linked
gene-2 interacting protein X), His-Domain type N23
protein tyrosine phosphatase (HD-PTP, also known as
PTPN23), RhoA-binding proteins Rhophilin-1 and -2, Brox,
Saccharomyces cerevisiae Bro1, Ustilago maydis Rim23
(also known as PalC), and related domains. Alix, HD-PTP,
Brox, Bro1, Rim20, and Rim23, interact with the ESCRT
(Endosomal Sorting Complexes Required for Transport)
system. Rim20 and Rim23 participate in the response to
the external pH via the Rim101 pathway. Bro1-like
domains are boomerang-shaped, and part of the domain is
a tetratricopeptide repeat (TPR)-like structure.
Bro1-like domains bind components of the ESCRT-III
complex: Snf7 in the case of Rim20. RIM20, and some
other members of the BRO1_Alix_like superfamily
including Alix, also have a V-shaped (V) domain. In the
case of Alix, the V-domain is a dimerization domain that
also contains a binding site for the retroviral late
assembly (L) domain YPXnL motif, which is partially
conserved in the V-domain superfamily. Rim20 localizes
to endosomes under alkaline pH conditions. By binding
Snf7, it may bring the protease Rim13 (a YPxL-containing
transcription factor) into proximity with Rim101, and
thus aid in the proteolytic activation of the latter.
Rim20 and other intermediates in the Rim101 pathway play
roles in the pathogenesis of fungal corneal infection
during Candida albicans keratitis.
Length = 355
Score = 28.8 bits (65), Expect = 3.5
Identities = 22/81 (27%), Positives = 32/81 (39%), Gaps = 12/81 (14%)
Query: 202 KVDRTNCMYKLASMYA-------DGPDENL-----LFQSTEGQLNLIETDYSKVLKPLLD 249
K +R N +Y L ++Y+ DE L FQ++ G I L P D
Sbjct: 102 KFERANILYNLGALYSQLALSENRYTDEGLKRACSYFQASAGCFEYILQHLLPTLSPPPD 161
Query: 250 LHLGRHHSIPMLLSALTQELF 270
L ++ L+ A QE F
Sbjct: 162 LDENTLKALESLMLAQAQECF 182
>gnl|CDD|218956 pfam06248, Zw10, Centromere/kinetochore Zw10. Zw10 and rough deal
proteins are both required for correct metaphase
check-pointing during mitosis. These proteins bind to
the centromere/kinetochore.
Length = 593
Score = 28.9 bits (65), Expect = 3.8
Identities = 26/112 (23%), Positives = 45/112 (40%), Gaps = 19/112 (16%)
Query: 108 PGQNSEKVAQQKVQELQMEADNNRETVKQMAGMQKLNSKIKSLE--LQGKRLREVYKAAK 165
A +++ EL+ + + +K + + K++ ++ L GK KAA
Sbjct: 73 EILQDLNDAVEELAELKRQLEEKILGLKILQKLLKIHEALEETNEALSGKDYL---KAAD 129
Query: 166 LNNKIKSL--ELQGKRLREV--YKAASQEFRETVYLLFGYKVDRTNCMYKLA 213
L K KSL L+ ++ E+ YK+ E Y V N +Y L
Sbjct: 130 LLEKAKSLLDGLKSRKGEELEIYKSLRLE----------YTVQSQNLLYHLG 171
>gnl|CDD|225638 COG3096, MukB, Uncharacterized protein involved in chromosome
partitioning [Cell division and chromosome partitioning].
Length = 1480
Score = 28.7 bits (64), Expect = 5.1
Identities = 17/64 (26%), Positives = 26/64 (40%), Gaps = 8/64 (12%)
Query: 110 QNSEKVAQQKVQELQMEADNNRETVKQM--------AGMQKLNSKIKSLELQGKRLREVY 161
+E+ A+ + EL + NR Q+ A M L K++ LE +RE
Sbjct: 1051 SGAEERARIRRDELHAQLSTNRSRRNQLEKQLTFCEAEMDNLTRKLRKLERDYFEMREQV 1110
Query: 162 KAAK 165
AK
Sbjct: 1111 VTAK 1114
>gnl|CDD|238105 cd00179, SynN, Syntaxin N-terminus domain; syntaxins are nervous
system-specific proteins implicated in the docking of
synaptic vesicles with the presynaptic plasma membrane;
they are a family of receptors for intracellular
transport vesicles; each target membrane may be
identified by a specific member of the syntaxin family;
syntaxins contain a moderately well conserved
amino-terminal domain, called Habc, whose structure is
an antiparallel three-helix bundle; a linker of about 30
amino acids connects this to the carboxy-terminal
region, designated H3 (t_SNARE), of the syntaxin
cytoplasmic domain; the highly conserved H3 region forms
a single, long alpha-helix when it is part of the core
SNARE complex and anchors the protein on the cytoplasmic
surface of cellular membranes; H3 is not included in
defining this domain.
Length = 151
Score = 27.6 bits (62), Expect = 5.1
Identities = 15/89 (16%), Positives = 40/89 (44%), Gaps = 12/89 (13%)
Query: 117 QQKVQELQMEADNNRETVKQMAGMQKLNSKIKSLELQGKRLREVY---------KAAKLN 167
++V+E++ N + + + +QKL+S++ + L++ A ++
Sbjct: 5 FEEVEEIR---GNIDKISEDVEELQKLHSQLLTAPDADPELKQELESLVQEIKKLAKEIK 61
Query: 168 NKIKSLELQGKRLREVYKAASQEFRETVY 196
K+K LE ++ + ++ R+T +
Sbjct: 62 GKLKELEESNEQNEALNGSSVDRIRKTQH 90
Score = 27.2 bits (61), Expect = 6.8
Identities = 16/87 (18%), Positives = 38/87 (43%), Gaps = 5/87 (5%)
Query: 110 QNSEKVAQQKVQELQMEADNNRETVKQMAGMQKLNSKIKSLELQGKRLREVYKAAKLNNK 169
+ A EL+ E ++ + +K++A ++ K+K LE ++ + ++ +
Sbjct: 29 HSQLLTAPDADPELKQELESLVQEIKKLAK--EIKGKLKELEESNEQNEALNGSSVDRIR 86
Query: 170 IKSLELQGKRLREV---YKAASQEFRE 193
K+ EV + A +++RE
Sbjct: 87 KTQHSGLSKKFVEVMTEFNKAQRKYRE 113
>gnl|CDD|218417 pfam05075, DUF684, Protein of unknown function (DUF684). This
family contains several uncharacterized proteins from
Caenorhabditis elegans. The GO annotation suggests that
the protein is involved in nematode larval development
and has a positive regulation on growth rate.
Length = 346
Score = 27.8 bits (62), Expect = 6.3
Identities = 13/28 (46%), Positives = 13/28 (46%)
Query: 135 KQMAGMQKLNSKIKSLELQGKRLREVYK 162
K M G KL KI LE K RE Y
Sbjct: 135 KNMYGPDKLKEKITELEELMKCWREEYN 162
>gnl|CDD|153336 cd07652, F-BAR_Rgd1, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Saccharomyces cerevisiae
Rho GTPase activating protein Rgd1 and similar proteins.
F-BAR domains are dimerization modules that bind and
bend membranes and are found in proteins involved in
membrane dynamics and actin reorganization.
Saccharomyces cerevisiae Rgd1 is a GTPase activating
protein (GAP) with activity towards Rho3p and Rho4p,
which are involved in bud growth and cytokinesis,
respectively. At low pH, S. cerevisiae Rgd1 is required
for cell survival and the activation of the protein
kinase C pathway, which is important in cell integrity
and the maintenance of cell shape. It contains an
N-terminal F-BAR domain and a C-terminal Rho GAP domain.
The F-BAR domain of S. cerevisiae Rgd1 binds to
phosphoinositides and plays an important role in the
localization of the protein to the bud tip/neck during
the cell cycle. F-BAR domains form banana-shaped dimers
with a positively-charged concave surface that binds to
negatively-charged lipid membranes. They can induce
membrane deformation in the form of long tubules.
Length = 234
Score = 27.7 bits (62), Expect = 6.5
Identities = 18/91 (19%), Positives = 35/91 (38%), Gaps = 15/91 (16%)
Query: 120 VQELQMEADNNRETVKQ------------MAGMQKLNSKIKSL--ELQGKRLREVYKAAK 165
+ L + +R+++K+ A +K ++ SL +L+ + + K K
Sbjct: 95 LSSLAKTVEKSRKSIKETGKRAEKKVQDAEAAAEKAKARYDSLADDLERVKTGDPGKKLK 154
Query: 166 LNNK-IKSLELQGKRLREVYKAASQEFRETV 195
K KS L +AA Q++ V
Sbjct: 155 FGLKGNKSAAQHEDELLRKVQAADQDYASKV 185
>gnl|CDD|218602 pfam05478, Prominin, Prominin. The prominins are an emerging
family of proteins that among the multispan membrane
proteins display a novel topology. Mouse prominin and
human prominin (mouse)-like 1 (PROML1) are predicted to
contain five membrane spanning domains, with an
N-terminal domain exposed to the extracellular space
followed by four, alternating small cytoplasmic and
large extracellular, loops and a cytoplasmic C-terminal
domain. The exact function of prominin is unknown
although in humans defects in PROM1, the gene coding for
prominin, cause retinal degeneration.
Length = 807
Score = 28.1 bits (63), Expect = 6.8
Identities = 14/77 (18%), Positives = 32/77 (41%), Gaps = 8/77 (10%)
Query: 121 QELQMEADNNRE-----TVKQMAGMQKLNSKIKSLELQGKRLREVYKAAKLNNKIKSLE- 174
L+ EA + R + ++KLNS +K+L+ L+ + ++++ +
Sbjct: 646 VALKNEALDLRSIQQNFVPPMESLLEKLNSNVKTLDESSNDLQN--AVKDVLAEVQAAQG 703
Query: 175 LQGKRLREVYKAASQEF 191
E+ S++F
Sbjct: 704 FLNNNASEIVNEESKKF 720
>gnl|CDD|198422 cd10464, PUB_RNF31, PNGase/UBA or UBX (PUB) domain of the RNF31 (or
HOIP) protein. This PUB domain is found in the p97
adaptor protein RNF31 (RING finger protein 31). The PUB
domain functions as a p97 (also known as
valosin-containing protein or VCP) adaptor by
interacting with the D1 and/or D2 ATPase domains. The
type II AAA+ ATPase p97 is involved in a variety of
cellular processes such as the deglycosylation of ERAD
substrates, membrane fusion, transcription factor
activation and cell cycle regulation through
differential binding to specific adaptor proteins. The
RNF31 protein, also known as HOIP or Zibra, contains an
N-terminal PUB domain similar to those in PNGase and
UBXD1, suggesting its association with p97. RNF31
functions in a complex with another RING-finger protein
(HOIL-IL), displaying E3 ubiquitin-protein ligase
activity, and forming linear ubiquitin chain assembly
complex (LUBAC) through linkages between the N- and
C-termini of ubiquitin. LUBAC has been shown to activate
the NF-kappaB pathway.
Length = 111
Score = 26.6 bits (59), Expect = 8.0
Identities = 19/65 (29%), Positives = 26/65 (40%), Gaps = 11/65 (16%)
Query: 191 FRETVYLLFGYKVDRTNCMYKLASMYADGPDENLLFQSTEGQLNLIETDYSKVLKPLLDL 250
FR V + G N + Y + + L F ++ E D SKV K LDL
Sbjct: 53 FRTKVDAVQG----GRNVLSLYG--YTESQPDGLSFPD-----DVEEPDISKVAKVTLDL 101
Query: 251 HLGRH 255
+ RH
Sbjct: 102 IVLRH 106
>gnl|CDD|236650 PRK10095, PRK10095, ribonuclease I; Provisional.
Length = 268
Score = 27.5 bits (61), Expect = 8.1
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 3/47 (6%)
Query: 17 VLVILVELGYLSSNRER---ERDELLREKELKEKVDHLTYQMEWRAL 60
VL + + G+ S +R E DE +KE K D LT W L
Sbjct: 38 VLALSWQTGFCQSQHDRNRNEPDECRLQKETTNKADFLTVHGLWPGL 84
>gnl|CDD|119407 cd02696, MurNAc-LAA, N-acetylmuramoyl-L-alanine amidase or
MurNAc-LAA (also known as peptidoglycan aminohydrolase,
NAMLA amidase, NAMLAA, Amidase 3, and peptidoglycan
amidase; EC 3.5.1.28) is an autolysin that hydrolyzes
the amide bond between N-acetylmuramoyl and L-amino
acids in certain cell wall glycopeptides. These proteins
are Zn-dependent peptidases with highly conserved
residues involved in cation co-ordination. MurNAc-LAA in
this family is one of several peptidoglycan hydrolases
(PGHs) found in bacterial and bacteriophage or prophage
genomes that are involved in the degradation of the
peptidoglycan. In Escherichia coli, there are five
MurNAc-LAAs present: AmiA, AmiB, AmiC and AmiD that are
periplasmic, and AmpD that is cytoplasmic. Three of
these (AmiA, AmiB and AmiC) belong to this family, the
other two (AmiD and AmpD) do not. E. coli AmiA, AmiB and
AmiC play an important role in cleaving the septum to
release daughter cells after cell division. In general,
bacterial MurNAc-LAAs are members of the bacterial
autolytic system and carry a signal peptide in their
N-termini that allows their transport across the
cytoplasmic membrane. However, the bacteriophage
MurNAc-LAAs are endolysins since these phage-encoded
enzymes break down bacterial peptidoglycan at the
terminal stage of the phage reproduction cycle. As
opposed to autolysins, almost all endolysins have no
signal peptides and their translocation through the
cytoplasmic membrane is thought to proceed with the help
of phage-encoded holin proteins. The amidase catalytic
module is fused to another functional module (cell wall
binding module or CWBM) either at the N- or C-terminus,
which is responsible for high affinity binding of the
protein to the cell wall.
Length = 172
Score = 26.7 bits (60), Expect = 9.5
Identities = 9/29 (31%), Positives = 18/29 (62%), Gaps = 3/29 (10%)
Query: 20 ILVELGYLSSNRERERDELLREKELKEKV 48
+LVELG++S+ + + L E ++K+
Sbjct: 138 VLVELGFISNPEDAKL---LNSPEYQDKI 163
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
0.314 0.130 0.352
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,872,036
Number of extensions: 1308783
Number of successful extensions: 1770
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1719
Number of HSP's successfully gapped: 151
Length of query: 284
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 188
Effective length of database: 6,679,618
Effective search space: 1255768184
Effective search space used: 1255768184
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 (21.5 bits)
S2: 58 (26.1 bits)