RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13263
(577 letters)
>gnl|CDD|213253 cd03286, ABC_MSH6_euk, ATP-binding cassette domain of eukaryotic
MutS6 homolog. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the MutS
family possess C-terminal domain with a conserved ATPase
activity that belongs to the ATP binding cassette (ABC)
superfamily. MutS homologs (MSH) have been identified in
most prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 218
Score = 118 bits (297), Expect = 2e-30
Identities = 46/97 (47%), Positives = 60/97 (61%), Gaps = 2/97 (2%)
Query: 390 RGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
RGT T+DG IA LE ++ + CLT+F+THYHS+ E V +M+ +D
Sbjct: 120 RGTSTHDGYAIAHAVLEYLVKKVKCLTLFSTHYHSLCDEFHEHGGVRLGHMACAVKNESD 179
Query: 449 G-IDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVK 484
I I FLYKLV GICPKS+G VA +AGIP+ VV+
Sbjct: 180 PTIRDITFLYKLVAGICPKSYGLYVALMAGIPDGVVE 216
>gnl|CDD|197777 smart00534, MUTSac, ATPase domain of DNA mismatch repair MUTS
family.
Length = 185
Score = 113 bits (285), Expect = 4e-29
Identities = 43/97 (44%), Positives = 59/97 (60%), Gaps = 6/97 (6%)
Query: 389 CRGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRN 447
RGT T DG IA LE L +IG T+FATHYH + + P V +MS +E+
Sbjct: 88 GRGTSTYDGLAIAAAILEYLLEKIGARTLFATHYHELTKLADNHPGVRNLHMSALEET-- 145
Query: 448 DGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVK 484
+ I FLYKL PG+ KS+G VA+LAG+P++V++
Sbjct: 146 ---ENITFLYKLKPGVAGKSYGIEVAKLAGLPKEVIE 179
>gnl|CDD|215944 pfam00488, MutS_V, MutS domain V. This domain is found in proteins
of the MutS family (DNA mismatch repair proteins) and is
found associated with pfam01624, pfam05188, pfam05192
and pfam05190. The mutS family of proteins is named
after the Salmonella typhimurium MutS protein involved
in mismatch repair; other members of the family included
the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have
various roles in DNA repair and recombination. Human MSH
has been implicated in non-polyposis colorectal
carcinoma (HNPCC) and is a mismatch binding protein. The
aligned region corresponds with domain V of Thermus
aquaticus MutS as characterized in, which contains a
Walker A motif, and is structurally similar to the
ATPase domain of ABC transporters.
Length = 235
Score = 102 bits (256), Expect = 1e-24
Identities = 45/108 (41%), Positives = 60/108 (55%), Gaps = 6/108 (5%)
Query: 390 RGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
RGT T DG IA E + I T+FATHYH + + + P V +M+ +E
Sbjct: 133 RGTSTYDGLAIAWAVAEHLAEKIRARTLFATHYHELTKLAEKLPAVKNVHMAAVET---- 188
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEAR 496
IVFLYK+ PG KS+G +VAELAG+PE VV+ V ++E R
Sbjct: 189 -NGDIVFLYKVKPGAADKSYGIHVAELAGLPESVVERAREVLAELEDR 235
>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 843
Score = 106 bits (268), Expect = 4e-24
Identities = 54/145 (37%), Positives = 80/145 (55%), Gaps = 12/145 (8%)
Query: 390 RGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
RGT T DG IA LE + IGC T+FATHYH + + P V +MS +E+
Sbjct: 697 RGTSTYDGLAIAWAVLEYLHEKIGCRTLFATHYHELTELEEKLPQVKNYHMSAVEEG--- 753
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARH-----NLRQLF 503
I FLYK+ PGI KS+G +VA+LAG+PE+V++ + ++E L Q
Sbjct: 754 --GDITFLYKVKPGIADKSYGIHVAKLAGLPEEVIERAREILAELEKESRSSNLELNQKD 811
Query: 504 IHKFASLVKSGEKVDVEEL-QKALE 527
+ F ++K+ + +D +EL +AL
Sbjct: 812 LSLFPKVLKALKSLDPDELTPRALN 836
Score = 66.5 bits (163), Expect = 2e-11
Identities = 23/45 (51%), Positives = 28/45 (62%)
Query: 203 LKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADEL 247
K TP M Q+ IK+Q D +LFF++G FYELF DA I A L
Sbjct: 3 KAKLTPMMQQYLEIKAQYPDTLLFFRMGDFYELFFEDAKIAARLL 47
Score = 46.5 bits (111), Expect = 3e-05
Identities = 27/110 (24%), Positives = 44/110 (40%), Gaps = 2/110 (1%)
Query: 279 FPDMSELLKYFENAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAH 338
++ELL+ E A + + + I K G + E DE+ D + + ++ I +
Sbjct: 398 LDYLAELLELLETAINEDPPLAVRDGIIKEGYNIELDELRDLLNNAKEWIAKLELEERER 457
Query: 339 FGCTVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPE 388
G K Y +EV A ++ R T KN E + TPE
Sbjct: 458 TGIK-SLKIKYNKVYGYYIEVTKSNAKLVPDDYIRRQT-LKNAERFTTPE 505
>gnl|CDD|213254 cd03287, ABC_MSH3_euk, ATP-binding cassette domain of eukaryotic
MutS3 homolog. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the MutS
family possess C-terminal domain with a conserved ATPase
activity that belongs to the ATP binding cassette (ABC)
superfamily. MutS homologs (MSH) have been identified in
most prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 222
Score = 98.7 bits (246), Expect = 2e-23
Identities = 43/99 (43%), Positives = 61/99 (61%), Gaps = 5/99 (5%)
Query: 390 RGTGTNDGCVIARVTLEKFLQI-GCLTVFATHYHSVARRLRE-EPNVAFEYMSYIEDKRN 447
RGT T+DG IA TL L+ CL +F THY S+ LR E ++ +MSY+E +++
Sbjct: 121 RGTSTHDGIAIAYATLHYLLEEKKCLVLFVTHYPSLGEILRRFEGSIRNYHMSYLESQKD 180
Query: 448 DGI---DTIVFLYKLVPGICPKSFGFNVAELAGIPEDVV 483
+I FLYKLV G+ +SFG NVA LAG+P+ ++
Sbjct: 181 FETSDSQSITFLYKLVRGLASRSFGLNVARLAGLPKSII 219
>gnl|CDD|213210 cd03243, ABC_MutS_homologs, ATP-binding cassette domain of MutS
homologs. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the MutS
family also possess a conserved ATPase activity that
belongs to the ATP binding cassette (ABC) superfamily.
MutS homologs (MSH) have been identified in most
prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 202
Score = 92.3 bits (230), Expect = 2e-21
Identities = 38/108 (35%), Positives = 53/108 (49%), Gaps = 13/108 (12%)
Query: 379 KNVENYVTPE--------CRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLRE 430
K + + TP RGT T +G IA LE L+ GC T+FATH+H +A +
Sbjct: 100 KEILSLATPRSLVLIDELGRGTSTAEGLAIAYAVLEHLLEKGCRTLFATHFHELADLPEQ 159
Query: 431 EPNVAFEYMSYIEDKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGI 478
P V +M + + F YKL+ GIC S+ +AELAG+
Sbjct: 160 VPGVKNLHMEELITT-----GGLTFTYKLIDGICDPSYALQIAELAGL 202
>gnl|CDD|213251 cd03284, ABC_MutS1, ATP-binding cassette domain of MutS1 homolog.
The MutS protein initiates DNA mismatch repair by
recognizing mispaired and unpaired bases embedded in
duplex DNA and activating endo- and exonucleases to
remove the mismatch. Members of the MutS family possess
C-terminal domain with a conserved ATPase activity that
belongs to the ATP binding cassette (ABC) superfamily.
MutS homologs (MSH) have been identified in most
prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 216
Score = 87.7 bits (218), Expect = 8e-20
Identities = 38/96 (39%), Positives = 54/96 (56%), Gaps = 6/96 (6%)
Query: 390 RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
RGT T DG IA +E +IG T+FATHYH + + P V +++ E
Sbjct: 120 RGTSTYDGLSIAWAIVEYLHEKIGAKTLFATHYHELTELEGKLPRVKNFHVAVKEKG--- 176
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVK 484
+VFL+K+V G KS+G VA LAG+PE+V++
Sbjct: 177 --GGVVFLHKIVEGAADKSYGIEVARLAGLPEEVIE 210
>gnl|CDD|235444 PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional.
Length = 854
Score = 90.9 bits (227), Expect = 5e-19
Identities = 56/159 (35%), Positives = 77/159 (48%), Gaps = 29/159 (18%)
Query: 390 RGTGTNDGCVIARVTLEKFL--QIGCLTVFATHYH---SVARRLREEPNVAFEYMSYIED 444
RGT T DG IA E +L +IG T+FATHYH + +L P V +++ E
Sbjct: 697 RGTSTYDGLSIAWAVAE-YLHDKIGAKTLFATHYHELTELEEKL---PGVKNVHVAVKEH 752
Query: 445 KRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFI 504
IVFL+K+VPG KS+G +VA+LAG+P V+K AR L QL
Sbjct: 753 G-----GDIVFLHKVVPGAADKSYGIHVAKLAGLPASVIK---------RAREILAQL-- 796
Query: 505 HKFASLVKSGEKVDVEELQKALESVKSFESQTKKDLEDL 543
S + + EE Q +L + ES + L+ L
Sbjct: 797 ---ESASEKAKAASAEEDQLSLFAEPE-ESPLLEALKAL 831
Score = 67.4 bits (166), Expect = 1e-11
Identities = 21/45 (46%), Positives = 28/45 (62%)
Query: 203 LKKQTPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADEL 247
+ K TP M Q+ IK+Q D +LFF++G FYELF DA + L
Sbjct: 5 MSKLTPMMQQYLEIKAQYPDALLFFRMGDFYELFFEDAKKASRLL 49
Score = 33.5 bits (78), Expect = 0.36
Identities = 27/103 (26%), Positives = 38/103 (36%), Gaps = 35/103 (33%)
Query: 302 GNIIPKAGVDKEYDE---VMDE----IKSIE-KEIQTYLRTQCAH--------FGCTVIY 345
G +I G D E DE + D + +E +E + RT + FG
Sbjct: 421 GGVI-ADGYDAELDELRALSDNGKDWLAELEARERE---RTGISSLKVGYNKVFG----- 471
Query: 346 SEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPE 388
Y +EV K ++ R T K N E Y+TPE
Sbjct: 472 ---------YYIEVTKANLDKVPEDYIRRQTLK-NAERYITPE 504
>gnl|CDD|213252 cd03285, ABC_MSH2_euk, ATP-binding cassette domain of eukaryotic
MutS2 homolog. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the MutS
family possess C-terminal domain with a conserved ATPase
activity that belongs to the ATP binding cassette (ABC)
superfamily. MutS homologs (MSH) have been identified in
most prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 222
Score = 80.5 bits (199), Expect = 3e-17
Identities = 40/106 (37%), Positives = 58/106 (54%), Gaps = 4/106 (3%)
Query: 390 RGTGTNDGCVIARVTLEKFL-QIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
RGT T DG +A E QI C +FATH+H + E PNV +++ + D D
Sbjct: 120 RGTSTYDGFGLAWAIAEYIATQIKCFCLFATHFHELTALADEVPNVKNLHVTALTD---D 176
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQME 494
T+ LYK+ G C +SFG +VAELA P++V++ A ++E
Sbjct: 177 ASRTLTMLYKVEKGACDQSFGIHVAELANFPKEVIEMAKQKALELE 222
>gnl|CDD|216613 pfam01624, MutS_I, MutS domain I. This domain is found in proteins
of the MutS family (DNA mismatch repair proteins) and is
found associated with pfam00488, pfam05188, pfam05192
and pfam05190. The MutS family of proteins is named
after the Salmonella typhimurium MutS protein involved
in mismatch repair; other members of the family included
the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have
various roles in DNA repair and recombination. Human MSH
has been implicated in non-polyposis colorectal
carcinoma (HNPCC) and is a mismatch binding protein. The
aligned region corresponds with globular domain I, which
is involved in DNA binding, in Thermus aquaticus MutS as
characterized in.
Length = 113
Score = 75.7 bits (187), Expect = 1e-16
Identities = 26/56 (46%), Positives = 33/56 (58%)
Query: 207 TPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGEST 262
TP M Q+ +KS+ D VLFF+VG FYELF DA I A EL + G +G+
Sbjct: 1 TPMMRQYLELKSKYPDAVLFFRVGDFYELFGEDAEIAARELGITLTVRGGGSGKRI 56
>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS. [DNA
metabolism, DNA replication, recombination, and repair].
Length = 840
Score = 74.8 bits (184), Expect = 5e-14
Identities = 38/112 (33%), Positives = 58/112 (51%), Gaps = 6/112 (5%)
Query: 390 RGTGTNDGCVIARVTLEKFLQ-IGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
RGT T DG +A E + I T+FATHY + P + +++ +E
Sbjct: 682 RGTSTYDGLALAWAIAEYLHEHIRAKTLFATHYFELTALEESLPGLKNVHVAALEHN--- 738
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLR 500
TIVFL++++PG KS+G VA LAG+P++V+ + Q+EAR
Sbjct: 739 --GTIVFLHQVLPGPASKSYGLAVAALAGLPKEVIARARQILTQLEARSTES 788
Score = 53.6 bits (129), Expect = 2e-07
Identities = 21/56 (37%), Positives = 30/56 (53%)
Query: 207 TPCMGQWWTIKSQNFDCVLFFKVGKFYELFHMDAVIGADELACSYMKESGCTGEST 262
TP M Q+ +K+++ D +LFF++G FYELF+ DA A L S E
Sbjct: 2 TPMMQQYLKLKAEHPDALLFFRMGDFYELFYEDAKKAAQLLDISLTSRGQSADEPI 57
Score = 35.5 bits (82), Expect = 0.075
Identities = 35/142 (24%), Positives = 59/142 (41%), Gaps = 31/142 (21%)
Query: 262 TLLTQLCNYESQTPSGCFPDMSELLKYFENAFDHKEASSAGNIIPKAGVDKE-YDEVMDE 320
LL +L Q + D SELL+ E A + ++ G+ +E YDE +DE
Sbjct: 365 ALLEELEGPTLQALAAQIDDFSELLELLEAAL----IENPPLVVRDGGLIREGYDEELDE 420
Query: 321 IKSIEKEIQTYLRTQCAHFGCTVIYSEAQKKQKK--------------YVLEVPSKYASK 366
+++ +E YL EA+++++ Y +EV
Sbjct: 421 LRAASREGTDYLARL-----------EARERERTGIPTLKVGYNAVFGYYIEVTRGQLHL 469
Query: 367 AKSNHQRVATKKKNVENYVTPE 388
++++R T KN E Y+TPE
Sbjct: 470 VPAHYRRRQT-LKNAERYITPE 490
>gnl|CDD|213248 cd03281, ABC_MSH5_euk, ATP-binding cassette domain of eukaryotic
MutS5 homolog. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the MutS
family possess C-terminal domain with a conserved ATPase
activity that belongs to the ATP binding cassette (ABC)
superfamily. MutS homologs (MSH) have been identified in
most prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 213
Score = 63.9 bits (156), Expect = 2e-11
Identities = 32/95 (33%), Positives = 48/95 (50%), Gaps = 6/95 (6%)
Query: 390 RGTGTNDGCVIARVTLEKFLQIG--C-LTVFATHYHSVARR--LREEPNVAFEYMS-YIE 443
+GT T DG + T+E L+ G C + +TH+H + R L E + F M +
Sbjct: 119 KGTDTEDGAGLLIATIEHLLKRGPECPRVIVSTHFHELFNRSLLPERLKIKFLTMEVLLN 178
Query: 444 DKRNDGIDTIVFLYKLVPGICPKSFGFNVAELAGI 478
+ I +LY+LVPG+ SF + A+LAGI
Sbjct: 179 PTSTSPNEDITYLYRLVPGLADTSFAIHCAKLAGI 213
>gnl|CDD|218487 pfam05190, MutS_IV, MutS family domain IV. This domain is found in
proteins of the MutS family (DNA mismatch repair
proteins) and is found associated with pfam01624,
pfam05188, pfam05192 and pfam00488. The mutS family of
proteins is named after the Salmonella typhimurium MutS
protein involved in mismatch repair; other members of
the family included the eukaryotic MSH 1,2,3, 4,5 and 6
proteins. These have various roles in DNA repair and
recombination. Human MSH has been implicated in
non-polyposis colorectal carcinoma (HNPCC) and is a
mismatch binding protein. The aligned region corresponds
in part with globular domain IV, which is involved in
DNA binding, in Thermus aquaticus MutS as characterized
in.
Length = 92
Score = 52.2 bits (126), Expect = 1e-08
Identities = 25/83 (30%), Positives = 37/83 (44%), Gaps = 8/83 (9%)
Query: 309 GVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCT---VIYSEAQKKQKKYVLEVPSKYAS 365
G D+E DE+ D ++ +E E+ L + G V Y+ K Y +EV A
Sbjct: 1 GFDEELDELRDLLEELESELDELLAKERERLGIKSLKVGYN----KVFGYYIEVTRSEAK 56
Query: 366 KAKSNHQRVATKKKNVENYVTPE 388
K ++ R T KN + TPE
Sbjct: 57 KVPKDYIRRQT-LKNGVRFTTPE 78
>gnl|CDD|218489 pfam05192, MutS_III, MutS domain III. This domain is found in
proteins of the MutS family (DNA mismatch repair
proteins) and is found associated with pfam00488,
pfam05188, pfam01624 and pfam05190. The MutS family of
proteins is named after the Salmonella typhimurium MutS
protein involved in mismatch repair; other members of
the family included the eukaryotic MSH 1,2,3, 4,5 and 6
proteins. These have various roles in DNA repair and
recombination. Human MSH has been implicated in
non-polyposis colorectal carcinoma (HNPCC) and is a
mismatch binding protein. The aligned region corresponds
with domain III, which is central to the structure of
Thermus aquaticus MutS as characterized in.
Length = 290
Score = 52.0 bits (125), Expect = 3e-07
Identities = 27/111 (24%), Positives = 46/111 (41%), Gaps = 2/111 (1%)
Query: 281 DMSELLKYFENAFD-HKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHF 339
+ ELL+ E A D S + K G D E DE+ + + +++ L +
Sbjct: 127 PLPELLELLERAIDEDPPLSLRDGGVIKDGYDPELDELRALLDELREKLAELLERERERT 186
Query: 340 GCTVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPECR 390
G + + YV+EV + A K ++ R + KN + TPE +
Sbjct: 187 GIKSLKVGYNRVFGYYVIEVKASKADKVPGDYIRR-STTKNAVRFTTPELK 236
>gnl|CDD|214710 smart00533, MUTSd, DNA-binding domain of DNA mismatch repair MUTS
family.
Length = 308
Score = 51.5 bits (124), Expect = 5e-07
Identities = 32/108 (29%), Positives = 52/108 (48%), Gaps = 10/108 (9%)
Query: 284 ELLKYFENAFDHKEASSAGNIIPKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGC-- 341
ELL N D E + G +I K G D E DE+ ++++ +E+E++ L+ + G
Sbjct: 122 ELLLELLNDDDPLEVND-GGLI-KDGFDPELDELREKLEELEEELEELLKKEREELGIDS 179
Query: 342 -TVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVATKKKNVENYVTPE 388
+ Y+ K Y +EV A K + R ++ KN E + TPE
Sbjct: 180 LKLGYN----KVHGYYIEVTKSEAKKVPKDFIRRSS-LKNTERFTTPE 222
>gnl|CDD|213250 cd03283, ABC_MutS-like, ATP-binding cassette domain of MutS-like
homolog. The MutS protein initiates DNA mismatch repair
by recognizing mispaired and unpaired bases embedded in
duplex DNA and activating endo- and exonucleases to
remove the mismatch. Members of the MutS family possess
C-terminal domain with a conserved ATPase activity that
belongs to the ATP binding cassette (ABC) superfamily.
MutS homologs (MSH) have been identified in most
prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 199
Score = 50.0 bits (120), Expect = 6e-07
Identities = 19/91 (20%), Positives = 37/91 (40%), Gaps = 7/91 (7%)
Query: 389 CRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMS-YIEDKRN 447
+GT + + + L+ + + +TH +A L + V + I+D
Sbjct: 115 FKGTNSRERQAASAAVLKFLKNKNTIGIISTHDLELADLLDLDSAVRNYHFREDIDD--- 171
Query: 448 DGIDTIVFLYKLVPGICPKSFGFNVAELAGI 478
+ ++F YKL PG+ P + + GI
Sbjct: 172 ---NKLIFDYKLKPGVSPTRNALRLMKKIGI 199
>gnl|CDD|213249 cd03282, ABC_MSH4_euk, ATP-binding cassette domain of eukaryotic
MutS4 homolog. The MutS protein initiates DNA mismatch
repair by recognizing mispaired and unpaired bases
embedded in duplex DNA and activating endo- and
exonucleases to remove the mismatch. Members of the MutS
family possess C-terminal domain with a conserved ATPase
activity that belongs to the ATP binding cassette (ABC)
superfamily. MutS homologs (MSH) have been identified in
most prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 204
Score = 43.5 bits (103), Expect = 9e-05
Identities = 23/73 (31%), Positives = 31/73 (42%), Gaps = 4/73 (5%)
Query: 390 RGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDG 449
RGT + DG I+ LE ++ FATH+ +A L + V +M N
Sbjct: 119 RGTSSADGFAISLAILECLIKKESTVFFATHFRDIAAILGNKSCVVHLHMKAQSINSNG- 177
Query: 450 IDTIVFLYKLVPG 462
I YKLV G
Sbjct: 178 ---IEMAYKLVLG 187
>gnl|CDD|224114 COG1193, COG1193, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 753
Score = 45.0 bits (107), Expect = 1e-04
Identities = 38/158 (24%), Positives = 67/158 (42%), Gaps = 14/158 (8%)
Query: 389 CRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
GT ++G +A LE L+ V THY + E V M +
Sbjct: 405 GSGTDPDEGAALAIAILEDLLEKPAKIVATTHYRELKALAAEREGVENASMEFDA----- 459
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFIHKFA 508
+T+ Y+L+ G+ +S F++A G+PE +++ T + L + I K
Sbjct: 460 --ETLRPTYRLLEGVPGRSNAFDIALRLGLPEPIIEEAKT---EFGEEKELLEELIEKLE 514
Query: 509 SLVKSGEKVDVEELQKALESVKSFE---SQTKKDLEDL 543
+ K + ++EE++K L+ V+ S K L +L
Sbjct: 515 EVRKE-LEEELEEVEKLLDEVELLTGANSGGKTSLLEL 551
>gnl|CDD|130141 TIGR01069, mutS2, MutS2 family protein. Function of MutS2 is
unknown. It should not be considered a DNA mismatch
repair protein. It is likely a DNA mismatch binding
protein of unknown cellular function [DNA metabolism,
Other].
Length = 771
Score = 43.3 bits (102), Expect = 3e-04
Identities = 38/155 (24%), Positives = 70/155 (45%), Gaps = 11/155 (7%)
Query: 389 CRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
GT ++G +A LE L+ + THY + + N E S + D
Sbjct: 412 GAGTDPDEGSALAISILEYLLKQNAQVLITTHYKEL--KALMYNNEGVENASVLFD---- 465
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFIHKFA 508
+T+ YKL+ GI +S+ F +A+ GIP +++ T + I K +
Sbjct: 466 -EETLSPTYKLLKGIPGESYAFEIAQRYGIPHFIIEQAKT---FYGEFKEEINVLIEKLS 521
Query: 509 SLVKSGEKVDVEELQKALESVKSFESQTKKDLEDL 543
+L K E+ E L+K L+ + + + ++++E+L
Sbjct: 522 ALEKELEQ-KNEHLEKLLKEQEKLKKELEQEMEEL 555
>gnl|CDD|213247 cd03280, ABC_MutS2, ATP-binding cassette domain of MutS2. MutS2
homologs in bacteria and eukaryotes. The MutS protein
initiates DNA mismatch repair by recognizing mispaired
and unpaired bases embedded in duplex DNA and activating
endo- and exonucleases to remove the mismatch. Members
of the MutS family also possess a conserved ATPase
activity that belongs to the ATP binding cassette (ABC)
superfamily. MutS homologs (MSH) have been identified in
most prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 200
Score = 39.5 bits (93), Expect = 0.002
Identities = 21/90 (23%), Positives = 37/90 (41%), Gaps = 7/90 (7%)
Query: 389 CRGTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRND 448
GT +G +A LE+ L+ G L + THY + + V M +
Sbjct: 118 GSGTDPVEGAALAIAILEELLERGALVIATTHYGELKAYAYKREGVENASMEF------- 170
Query: 449 GIDTIVFLYKLVPGICPKSFGFNVAELAGI 478
+T+ Y+L+ G+ +S +A G+
Sbjct: 171 DPETLKPTYRLLIGVPGRSNALEIARRLGL 200
>gnl|CDD|218440 pfam05110, AF-4, AF-4 proto-oncoprotein. This family consists of
AF4 (Proto-oncogene AF4) and FMR2 (Fragile X E mental
retardation syndrome) nuclear proteins. These proteins
have been linked to human diseases such as acute
lymphoblastic leukaemia and mental retardation. The
family also contains a Drosophila AF4 protein homologue
Lilliputian which contains an AT-hook domain.
Lilliputian represents a novel pair-rule gene that acts
in cytoskeleton regulation, segmentation and
morphogenesis in Drosophila.
Length = 1154
Score = 38.7 bits (90), Expect = 0.009
Identities = 32/168 (19%), Positives = 55/168 (32%), Gaps = 13/168 (7%)
Query: 5 SKESPEKKGDSESST---PASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDS 61
K+ EK+G +SS SK S + K P K+ KS QS++
Sbjct: 471 IKQPMEKEGKVKSSGSQYHPESKEPPPKSSSKEKRRPRTAQKGPESGRGKQ-KSPAQSEA 529
Query: 62 EPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKR 121
P + G + P KA E E E + + G+++
Sbjct: 530 PPQR--RTVGKKQPKKPEKASAGDERTGLRPESEPGTLPYGSSVQTPPDRPKAATKGSRK 587
Query: 122 GLSSKSGQPT-------KKPKLTAPSTPSTPSFPVSDTSETTPSTSGA 162
K + + +K K + P + F +D+S + +
Sbjct: 588 PSPRKEPKSSVPPAAEKRKYKSPSKIVPKSREFIETDSSSSDSPEDES 635
Score = 33.7 bits (77), Expect = 0.30
Identities = 36/172 (20%), Positives = 52/172 (30%), Gaps = 17/172 (9%)
Query: 4 DSKESPEKKGDSESSTPA---SSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSD 60
K+S S T + SSKGK+ K+ E D +K+ R + S S
Sbjct: 724 AEKDSLSAPKKQTSKTASEKSSSKGKRKHKNDE--EADKIESKKQRLEEKSSSCSPSSSS 781
Query: 61 SEPDDMLQDNG------SEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTP 114
S E+E +P + S S + SSS
Sbjct: 782 SHHHSSSNKESRKSSRNKEEEMLPSPSSPLSSSSPKPEHPSRKRPRRQEDTSSSSG---- 837
Query: 115 MKNGNKRGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGAQDWS 166
SS T K + T ST S +S TP+ + +
Sbjct: 838 -PFSASSTKSSSKSSSTSKHRKTEGKGSST-SKEHKGSSGDTPNKASSFPVP 887
>gnl|CDD|236304 PRK08581, PRK08581, N-acetylmuramoyl-L-alanine amidase; Validated.
Length = 619
Score = 37.5 bits (87), Expect = 0.018
Identities = 32/181 (17%), Positives = 58/181 (32%), Gaps = 26/181 (14%)
Query: 5 SKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSA----KRVKSAIQSD 60
+ +K D E+S SSK + + S D+ K S+ + I +
Sbjct: 39 TSHDSKKSNDDETSKDTSSKDTDKADNNNTSNQDNNDKKFSTIDSSTSDSNNIIDFIYKN 98
Query: 61 SEPDDMLQD---NGSEDEYVPP-----------------KAEVESESEHSSGEEELEESV 100
++ Q N +D Y + +S + S +
Sbjct: 99 LPQTNINQLLTKNKYDDNYSLTTLIQNLFNLNSDISDYEQPRNSEKSTNDSNKNSDSSIK 158
Query: 101 EDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPKLTAPSTPSTP-SFPVSDTSETTPST 159
D SS+ + + ++K K+P P+ P+ S P SD + S+
Sbjct: 159 NDTDTQSSKQDKADNQKAPSS-NNTKPSTSNKQPNSPKPTQPNQSNSQPASDDTANQKSS 217
Query: 160 S 160
S
Sbjct: 218 S 218
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 37.1 bits (87), Expect = 0.027
Identities = 37/154 (24%), Positives = 63/154 (40%), Gaps = 31/154 (20%)
Query: 391 GTGTNDGCVIARVTLEKFLQIGCLTVFATHYHSVARRLREEPNVAFEYMSYIEDKRNDGI 450
GT ++G +A LE + G + THY + + V E S D
Sbjct: 419 GTDPDEGAALAISILEYLRKRGAKIIATTHYKELKALMYNREGV--ENASVEFD-----E 471
Query: 451 DTIVFLYKLVPGICPKSFGFNVAELAGIPEDVVKFGTTVAFQMEARHNLRQLFIHKFASL 510
+T+ Y+L+ GI KS F +A+ G+PE++++ EA+ +
Sbjct: 472 ETLRPTYRLLIGIPGKSNAFEIAKRLGLPENIIE---------EAKKLI----------- 511
Query: 511 VKSGEKVDVEELQKALESVKSFESQTK-KDLEDL 543
+K + EL +LE E + K ++ E L
Sbjct: 512 --GEDKEKLNELIASLEE-LERELEQKAEEAEAL 542
>gnl|CDD|114270 pfam05539, Pneumo_att_G, Pneumovirinae attachment membrane
glycoprotein G.
Length = 408
Score = 36.2 bits (83), Expect = 0.040
Identities = 27/140 (19%), Positives = 44/140 (31%), Gaps = 12/140 (8%)
Query: 22 SSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKA 81
K K P + S T P S S + S+P + ++ +
Sbjct: 158 RGKDVSCCKEPKTAVTTSKTTSWPTEVSHPTYPSQVTPQSQPATQGHQTATANQRLSSTE 217
Query: 82 EVESE--SEHSSGEEELE--ESVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPKLT 137
V ++ + S+ E + E S P+ S T ++ + G + Q
Sbjct: 218 PVGTQGTTTSSNPEPQTEPPPSQRGPSGSPQHPPSTTSQDQSTTGDGQEHTQ-------- 269
Query: 138 APSTPSTPSFPVSDTSETTP 157
TP S S S TP
Sbjct: 270 RRKTPPATSNRRSPHSTATP 289
>gnl|CDD|218115 pfam04502, DUF572, Family of unknown function (DUF572). Family of
eukaryotic proteins with undetermined function.
Length = 321
Score = 34.7 bits (80), Expect = 0.12
Identities = 21/125 (16%), Positives = 42/125 (33%), Gaps = 5/125 (4%)
Query: 36 EDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEE 95
E+D + K D + +D +DN + + + +
Sbjct: 189 EEDEALIKSLSFGPETEEDRRRADDEDSEDDEEDNDNTPSPKSGSSSPAKPTS----ILK 244
Query: 96 LEESVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSET 155
+ PSSS+A+ R + S KK + S + + P S++ +T
Sbjct: 245 KSAAKRSEAPSSSKAKKNSRGIPKPRD-ALSSLVVRKKAAPESTSQSPSSAEPTSESPQT 303
Query: 156 TPSTS 160
++S
Sbjct: 304 AGNSS 308
>gnl|CDD|223039 PHA03307, PHA03307, transcriptional regulator ICP4; Provisional.
Length = 1352
Score = 35.1 bits (81), Expect = 0.13
Identities = 25/157 (15%), Positives = 43/157 (27%), Gaps = 5/157 (3%)
Query: 7 ESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDM 66
++ DS SS + ++ P + R S S+ +
Sbjct: 231 DAGASSSDSSSSESSGCGWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSS- 289
Query: 67 LQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRG-LSS 125
P S E + S+S + + G S
Sbjct: 290 -SPRERSPSPSPSSPGSGPAPSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGPSPS 348
Query: 126 KSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGA 162
+S P++ P PS+P P S +P+ S
Sbjct: 349 RSPSPSRPPPPADPSSPRKRPRPSRAPS--SPAASAG 383
Score = 32.8 bits (75), Expect = 0.62
Identities = 27/158 (17%), Positives = 46/158 (29%), Gaps = 3/158 (1%)
Query: 8 SPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDML 67
SP + + A+S SP + SP R + S+ S S
Sbjct: 188 SPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRSAADDAGASSSDSSSSESSGC 247
Query: 68 QDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPT--PSSSEAEVTPMKNGNKRGLSS 125
+ +P A + + S SSS E +P + + G
Sbjct: 248 GWGPENECPLPRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGP 307
Query: 126 KSGQPTKKPKLTAPSTPSTPS-FPVSDTSETTPSTSGA 162
P ++ S+ S S++S + G
Sbjct: 308 APSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGP 345
Score = 29.8 bits (67), Expect = 5.5
Identities = 17/111 (15%), Positives = 28/111 (25%), Gaps = 5/111 (4%)
Query: 59 SDSEPDDMLQDNGSEDEYVPPKAE-VESESEHSSGEEELEESVEDPTPSSSEAEVTPMKN 117
DD+L GS+ + V AE + + E P P
Sbjct: 28 PGDAADDLLS--GSQGQLVSDSAELAAVTVVAGAAACDRFEPPTGPPPGPGTEAPANESR 85
Query: 118 GNK--RGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGAQDWS 166
+ P ++ T P S P + + P +
Sbjct: 86 STPTWSLSTLAPASPAREGSPTPPGPSSPDPPPPTPPPASPPPSPAPDLSE 136
>gnl|CDD|220102 pfam09073, BUD22, BUD22. BUD22 has been shown in yeast to be a
nuclear protein involved in bud-site selection. It plays
a role in positioning the proximal bud pole signal. More
recently it has been shown to be involved in ribosome
biogenesis.
Length = 424
Score = 34.8 bits (80), Expect = 0.13
Identities = 38/152 (25%), Positives = 58/152 (38%), Gaps = 27/152 (17%)
Query: 4 DSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSD--S 61
+ E K S+ S+ + SKS +EDDS + S+ S
Sbjct: 156 KKSKKKEAKESSDKDDEEESESEDESKSEESAEDDS----------DDEEEEDSDSEDYS 205
Query: 62 EPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKR 121
+ D ML S DE +A + +E + E E +ES + + S S ++
Sbjct: 206 QYDGML--VDSSDEEEGEEAPSINYNE-DTSESESDESDSEISESRSVSD---------- 252
Query: 122 GLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTS 153
S +S P+KKPK S+ PS S
Sbjct: 253 --SEESSPPSKKPKEKKTSSTFLPSLMGGYFS 282
>gnl|CDD|220972 pfam11081, DUF2890, Protein of unknown function (DUF2890). This
family is conserved in dsDNA adenoviruses of
vertebrates. The function is not known.
Length = 172
Score = 33.4 bits (76), Expect = 0.15
Identities = 27/111 (24%), Positives = 45/111 (40%), Gaps = 13/111 (11%)
Query: 44 RPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELE-ESVED 102
P+ + K D +D S+ E V E + E S EE+ E E VE+
Sbjct: 2 PPKGNA----KKLKVRPPPTKDEEEDWDSQAEEVEEDEEEMEDWEDSLDEEDEEAEEVEE 57
Query: 103 PTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPK--------LTAPSTPSTP 145
T +SS+A + K+ ++ +S P ++P P+T + P
Sbjct: 58 ETAASSKAPSSSSKSSSQETISIPPTPPARRPSRRWDQTGRFPNPTTGAKP 108
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 34.5 bits (79), Expect = 0.15
Identities = 28/148 (18%), Positives = 50/148 (33%), Gaps = 16/148 (10%)
Query: 6 KESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDD 65
+E + S SS P+ + SP+ + +S + + + E ++
Sbjct: 407 QERERQGTSSRSSDPSKASSTSGE-SPSMASQESEEEESVEE----------EEEEEEEE 455
Query: 66 MLQDNGSEDEYVPPKAEVESESEHSSGEEELE---ESVEDPTPSSSEAEVTPMKNGNKRG 122
++ SE+E + E E + EEE+E E D +AE +
Sbjct: 456 EEEEQESEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEPEEDAERR--NSEMAGI 513
Query: 123 LSSKSGQPTKKPKLTAPSTPSTPSFPVS 150
GQ + + S P P S
Sbjct: 514 SRMSEGQQPRGSSVQPESPQEEPLQPES 541
Score = 32.6 bits (74), Expect = 0.68
Identities = 32/161 (19%), Positives = 52/161 (32%), Gaps = 7/161 (4%)
Query: 6 KESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDD 65
E E + + E + G + + D + + I SE
Sbjct: 462 SEEEEGEDEEEEEEVEADNGSEEEMEGSSEGDGDGEEPEEDAERRNSEMAGISRMSEGQ- 520
Query: 66 MLQDNGSEDEYVPPKAEVESES--EHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGL 123
S P + ++ ES S GEE EE + + +P SS E+ + + +
Sbjct: 521 -QPRGSSVQPESPQEEPLQPESMDAESVGEESDEELLAEESPLSSHTELEGVATPVETKI 579
Query: 124 SSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGAQD 164
SS P P + S + + S T S QD
Sbjct: 580 SSSRKLP---PPPVSTSLENDSATVTSTTRNGNVSPHTPQD 617
>gnl|CDD|240271 PTZ00108, PTZ00108, DNA topoisomerase 2-like protein; Provisional.
Length = 1388
Score = 34.6 bits (80), Expect = 0.17
Identities = 19/107 (17%), Positives = 38/107 (35%), Gaps = 7/107 (6%)
Query: 5 SKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPD 64
SK + + + K K K S K+ +K+A++ KS +
Sbjct: 1289 SKRPDGESNGGSKPSSPTKKKVK--KRLEGSLAALKKKKKSEKKTARKKKS----KTRVK 1342
Query: 65 DMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAE 111
S P K + +S SE + E+++S ++ + +
Sbjct: 1343 QASASQSSRLLRRPRKKKSDSSSE-DDDDSEVDDSEDEDDEDDEDDD 1388
>gnl|CDD|235640 PRK05901, PRK05901, RNA polymerase sigma factor; Provisional.
Length = 509
Score = 33.8 bits (78), Expect = 0.23
Identities = 19/117 (16%), Positives = 38/117 (32%), Gaps = 9/117 (7%)
Query: 4 DSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQS---- 59
+S +K + + A + KK K S + + I
Sbjct: 71 ESDIPKKKTKTAAKAAAAKAPAKKKLKDELDSSKKAEKKNALDKDDDLNYVKDIDVLNQA 130
Query: 60 -----DSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAE 111
D + DD+ D+ +D+ E + + + +EE +E+ E S +
Sbjct: 131 DDDDDDDDDDDLDDDDIDDDDDDEDDDEDDDDDDVDDEDEEKKEAKELEKLSDDDDF 187
>gnl|CDD|218601 pfam05477, SURF2, Surfeit locus protein 2 (SURF2). Surfeit locus
protein 2 is part of a group of at least six sequence
unrelated genes (Surf-1 to Surf-6). The six Surfeit
genes have been classified as housekeeping genes, being
expressed in all tissue types tested and not containing
a TATA box in their promoter region. The exact function
of SURF2 is unknown.
Length = 244
Score = 32.6 bits (74), Expect = 0.41
Identities = 26/103 (25%), Positives = 40/103 (38%), Gaps = 7/103 (6%)
Query: 34 KSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGE 93
+ ED ++P R S+ DD ++ D Y P E + + G+
Sbjct: 133 RREDQEDGVRQPGRTEKSGSDFWEPPSSDEDDSDSEDSMSDLYPP-----ELFTLKNPGK 187
Query: 94 EELEESVED-PTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPK 135
E+ + +D T E EV + KR +SG TKK K
Sbjct: 188 EQNGDEDDDFETDDEDEMEVESPELQQKRS-KKQSGSLTKKFK 229
>gnl|CDD|218752 pfam05793, TFIIF_alpha, Transcription initiation factor IIF, alpha
subunit (TFIIF-alpha). Transcription initiation factor
IIF, alpha subunit (TFIIF-alpha) or RNA polymerase
II-associating protein 74 (RAP74) is the large subunit
of transcription factor IIF (TFIIF), which is essential
for accurate initiation and stimulates elongation by RNA
polymerase II.
Length = 528
Score = 33.0 bits (75), Expect = 0.50
Identities = 35/163 (21%), Positives = 53/163 (32%), Gaps = 6/163 (3%)
Query: 6 KESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDD 65
K SPE E S+ + K+ + K + K K SDS D
Sbjct: 303 KLSPEIPAKPEIEQDEDSEESEEEKNEEEGGLSKKGKKLKKLKGKKNGLDKDDSDSGDDS 362
Query: 66 MLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSS 125
D ED A + + EE ++ + P S K+ KR
Sbjct: 363 DDSDIDGEDSVSLVTA---KKQKEPKKEEPVDSNPSSPGNSGPARPSPESKDKGKRKA-- 417
Query: 126 KSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGAQDWSHN 168
+ + +K P T + P S + ++TP T S N
Sbjct: 418 -ANEVSKSPASVPAKKLKTENAPKSSSGKSTPQTFSGSKSSSN 459
>gnl|CDD|220365 pfam09726, Macoilin, Transmembrane protein. This entry is a highly
conserved protein present in eukaryotes.
Length = 680
Score = 33.0 bits (75), Expect = 0.53
Identities = 33/185 (17%), Positives = 56/185 (30%), Gaps = 15/185 (8%)
Query: 8 SPEKKGDSESSTPASSKGK-----KTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSE 62
S K SE+S+ + K + S S S K + +
Sbjct: 210 SVTDKEKSEASSKGLTSTKELVPVQNSGGNHSLSKSSNSQTPELEYSEKGKDHHHSHNHQ 269
Query: 63 PDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPT-----PSSSEAEVTPMKN 117
+ +N +E HS+ S SS+ A K+
Sbjct: 270 HHSIGINNHHSKHADSKLQTIEVIENHSNKSRPSSSSTNGSKETTSNSSSAAAGSIGSKS 329
Query: 118 GNKRGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSE----TTPSTSGAQDWSHNHYQFL 173
S+++ + PK + + S PS VSD + S+SGA+D +
Sbjct: 330 SKSAKHSNRNKSNS-SPKSHSSANGSVPSSSVSDNESKQKRASKSSSGARDSKKDASGMS 388
Query: 174 HPDHI 178
+
Sbjct: 389 ANGTV 393
>gnl|CDD|220648 pfam10243, MIP-T3, Microtubule-binding protein MIP-T3. This
protein, which interacts with both microtubules and
TRAF3 (tumour necrosis factor receptor-associated factor
3), is conserved from worms to humans. The N-terminal
region is the microtubule binding domain and is
well-conserved; the C-terminal 100 residues, also
well-conserved, constitute the coiled-coil region which
binds to TRAF3. The central region of the protein is
rich in lysine and glutamic acid and carries KKE motifs
which may also be necessary for tubulin-binding, but
this region is the least well-conserved.
Length = 506
Score = 32.9 bits (75), Expect = 0.53
Identities = 34/168 (20%), Positives = 53/168 (31%), Gaps = 11/168 (6%)
Query: 6 KESPEKKGDSES---STPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSE 62
KE P+ + E P K K+ K + D KR R ++ R K +
Sbjct: 125 KEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPP 184
Query: 63 PDDMLQDNGSED-----EYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKN 117
+ E V K E +E EE+ + E T E E
Sbjct: 185 NKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEEDDGKDRETTTSPMEEDESRQSSE 244
Query: 118 GNKRGLSSKS---GQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGA 162
++R SS P+ T S+ T + P + + + A
Sbjct: 245 ISRRSSSSLKKPDPSPSMASPETRESSKRTETRPRTSLRPPSARPASA 292
Score = 32.2 bits (73), Expect = 0.94
Identities = 21/124 (16%), Positives = 41/124 (33%), Gaps = 3/124 (2%)
Query: 20 PASSKGKKTSKSPAKSEDDSPVTKRPRRK---SAKRVKSAIQSDSEPDDMLQDNGSEDEY 76
SKG PAK + + + K ++ K + EP D ++++
Sbjct: 82 KGGSKGPAAKTKPAKEPKNESGKEEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKR 141
Query: 77 VPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPKL 136
P + E E E + + EE + + S + P K + + ++
Sbjct: 142 PPKEKEKEKEKKVEEPRDREEEKKRERVRAKSRPKKPPKKKPPNKKKEPPEEEKQRQAAR 201
Query: 137 TAPS 140
A
Sbjct: 202 EAVK 205
Score = 29.1 bits (65), Expect = 6.8
Identities = 27/161 (16%), Positives = 49/161 (30%), Gaps = 6/161 (3%)
Query: 6 KESPEKKGDSESSTPASSKGKKTSKSP-AKSEDDSPVTKRPR-RKSAKRVKSAIQSDSEP 63
+E EK+ E K K+ K K E + + ++ K+V+ + E
Sbjct: 105 EEEKEKEQVKEEKKKKKEKPKEEPKDRKPKEEAKEKRPPKEKEKEKEKKVEEPRDREEEK 164
Query: 64 D-DMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRG 122
+ ++ + P + + EEE + E + K
Sbjct: 165 KRERVRAKSRPKK---PPKKKPPNKKKEPPEEEKQRQAAREAVKGKPEEPDVNEEREKEE 221
Query: 123 LSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGAQ 163
K + T P S S+ S +S P S +
Sbjct: 222 DDGKDRETTTSPMEEDESRQSSEISRRSSSSLKKPDPSPSM 262
>gnl|CDD|215521 PLN02967, PLN02967, kinase.
Length = 581
Score = 32.7 bits (74), Expect = 0.57
Identities = 17/88 (19%), Positives = 30/88 (34%)
Query: 7 ESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDM 66
TP ++ K + S E+ + R RRK K + SE +
Sbjct: 101 NEDAALDKESKKTPRRTRRKAAAASSDVEEEKTEKKVRKRRKVKKMDEDVEDQGSESEVS 160
Query: 67 LQDNGSEDEYVPPKAEVESESEHSSGEE 94
+ + ++E E + E GE+
Sbjct: 161 DVEESEFVTSLENESEEELDLEKDDGED 188
>gnl|CDD|177653 PLN00014, PLN00014, light-harvesting-like protein 3; Provisional.
Length = 250
Score = 32.1 bits (73), Expect = 0.64
Identities = 22/124 (17%), Positives = 37/124 (29%), Gaps = 23/124 (18%)
Query: 77 VPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPKL 136
+ K+E S + + S P+P + G G ++ P
Sbjct: 29 LGAKSEGSLVSVTVASTDGGGISERKPSP--------LERGGTLEGEAAAGKDPGPAAAA 80
Query: 137 TAPSTPSTPSFP----VSDTSETTP-STSGAQDWSHNHYQFLHPDHILDADRRSPKHPDY 191
S F + T + G DW D ++DA+ K +
Sbjct: 81 KTSLAVSVGKFEDPRWKNGTWDLNQFKKDGKTDW----------DAVIDAEVVRRKWLED 130
Query: 192 NPKT 195
NP+T
Sbjct: 131 NPET 134
>gnl|CDD|148051 pfam06213, CobT, Cobalamin biosynthesis protein CobT. This family
consists of several bacterial cobalamin biosynthesis
(CobT) proteins. CobT is involved in the transformation
of precorrin-3 into cobyrinic acid.
Length = 282
Score = 32.1 bits (73), Expect = 0.69
Identities = 25/108 (23%), Positives = 37/108 (34%), Gaps = 28/108 (25%)
Query: 3 LDSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSE 62
L S + E+ GD S + S ++D P + D +
Sbjct: 203 LSSMDMAEELGDEPES----------ADSEDNEDEDDP-----------------KEDED 235
Query: 63 PDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEA 110
DD ++ S + S E SGE E E+ D TP S +A
Sbjct: 236 -DDQGEEEESGSSDSLSEDSDASSEEMESGEMEAAEASADDTPDSDDA 282
>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit. This model
describes Pseudomonas denitrificans CobT gene product,
which is a cobalt chelatase subunit that functions in
cobalamin biosynthesis. Cobalamin (vitamin B12) can be
synthesized via several pathways, including an aerobic
pathway (found in Pseudomonas denitrificans) and an
anaerobic pathway (found in P. shermanii and Salmonella
typhimurium). These pathways differ in the point of
cobalt insertion during corrin ring formation. There are
apparently a number of variations on these two pathways,
where the major differences seem to be concerned with
the process of ring contraction. Confusion regarding the
functions of enzymes found in the aerobic vs. anaerobic
pathways has arisen because nonhomologous genes in these
different pathways were given the same gene symbols.
Thus, cobT in the aerobic pathway (P. denitrificans) is
not a homolog of cobT in the anaerobic pathway (S.
typhimurium). It should be noted that E. coli
synthesizes cobalamin only when it is supplied with the
precursor cobinamide, which is a complex intermediate.
Additionally, all E. coli cobalamin synthesis genes
(cobU, cobS and cobT) were named after their Salmonella
typhimurium homologs which function in the anaerobic
cobalamin synthesis pathway. This model describes the
aerobic cobalamin pathway Pseudomonas denitrificans CobT
gene product, which is a cobalt chelatase subunit, with
a MW ~70 kDa. The aerobic pathway cobalt chelatase is a
heterotrimeric, ATP-dependent enzyme that catalyzes
cobalt insertion during cobalamin biosynthesis. The
other two subunits are the P. denitrificans CobS
(TIGR01650) and CobN (pfam02514 CobN/Magnesium
Chelatase) proteins. To avoid potential confusion with
the nonhomologous Salmonella typhimurium/E.coli cobT
gene product, the P. denitrificans gene symbol is not
used in the name of this model [Biosynthesis of
cofactors, prosthetic groups, and carriers, Heme,
porphyrin, and cobalamin].
Length = 600
Score = 32.6 bits (74), Expect = 0.71
Identities = 24/118 (20%), Positives = 40/118 (33%), Gaps = 29/118 (24%)
Query: 3 LDSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSE 62
L S E E+ GD S +DD P + +
Sbjct: 194 LRSMELAEEMGDDTESEDEE-----------DGDDDQP-----------------TENEQ 225
Query: 63 PDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNK 120
++ + G E P+ ++ E SGEEE+ +S +D P S+ + G +
Sbjct: 226 -EEQGEGEGEGQEGSAPQESEATDRESESGEEEMVQSDQDDLPDESDDDSETPGEGAR 282
>gnl|CDD|191716 pfam07263, DMP1, Dentin matrix protein 1 (DMP1). This family
consists of several mammalian dentin matrix protein 1
(DMP1) sequences. The dentin matrix acidic
phosphoprotein 1 (DMP1) gene has been mapped to human
chromosome 4q21. DMP1 is a bone and teeth specific
protein initially identified from mineralised dentin.
DMP1 is primarily localised in the nuclear compartment
of undifferentiated osteoblasts. In the nucleus, DMP1
acts as a transcriptional component for activation of
osteoblast-specific genes like osteocalcin. During the
early phase of osteoblast maturation, Ca(2+) surges into
the nucleus from the cytoplasm, triggering the
phosphorylation of DMP1 by a nuclear isoform of casein
kinase II. This phosphorylated DMP1 is then exported out
into the extracellular matrix, where it regulates
nucleation of hydroxyapatite. DMP1 is a unique molecule
that initiates osteoblast differentiation by
transcription in the nucleus and orchestrates
mineralised matrix formation extracellularly, at later
stages of osteoblast maturation. The DMP1 gene has been
found to be ectopically expressed in lung cancer
although the reason for this is unknown.
Length = 514
Score = 32.3 bits (73), Expect = 0.73
Identities = 40/158 (25%), Positives = 65/158 (41%), Gaps = 6/158 (3%)
Query: 7 ESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQ----SDSE 62
+S E + + + SS+ SE V R + S + S+S
Sbjct: 320 QSQEDSQEVQDPSSESSQEADLPSQENSSESQEEVVSESRGDNPDNTTSHSEDQEDSESS 379
Query: 63 PDDMLQDNGSEDEYVPPKAEVESESEHS-SGEEELEESVEDPTPSSSEAEVTPMKNGNKR 121
+D L D S E + + +SES S S EE ES ED SS E + + R
Sbjct: 380 EEDSL-DTPSSSESQSTEEQADSESNESLSSSEESPESTEDENSSSQEGLQSHSASTESR 438
Query: 122 GLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPST 159
S+S Q ++ + + S S+ S S+++E+ S+
Sbjct: 439 SQESQSEQDSRSEEDDSDSQDSSRSKEDSNSTESASSS 476
>gnl|CDD|233191 TIGR00927, 2A1904, K+-dependent Na+/Ca+ exchanger. [Transport and
binding proteins, Cations and iron carrying compounds].
Length = 1096
Score = 32.3 bits (73), Expect = 0.80
Identities = 21/109 (19%), Positives = 50/109 (45%), Gaps = 4/109 (3%)
Query: 6 KESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKS---AKRVKSAIQSDSE 62
E+ + G+ ES A +G+ +K +SE + P ++ ++ + ++ + ++E
Sbjct: 653 TEAEGENGE-ESGGEAEQEGETETKGENESEGEIPAERKGEQEGEGEIEAKEADHKGETE 711
Query: 63 PDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAE 111
+++ + +E E + E+E+ E E+E E E +E +
Sbjct: 712 AEEVEHEGETEAEGTEDEGEIETGEEGEEVEDEGEGEAEGKHEVETEGD 760
>gnl|CDD|221185 pfam11719, Drc1-Sld2, DNA replication and checkpoint protein.
Genome duplication is precisely regulated by
cyclin-dependent kinases CDKs, which bring about the
onset of S phase by activating replication origins and
then prevent relicensing of origins until mitosis is
completed. The optimum sequence motif for CDK
phosphorylation is S/T-P-K/R-K/R, and Drc1-Sld2 is found
to have at least 11 potential phosphorylation sites.
Drc1 is required for DNA synthesis and S-M replication
checkpoint control. Drc1 associates with Cdc2 and is
phosphorylated at the onset of S phase when Cdc2 is
activated. Thus Cdc2 promotes DNA replication by
phosphorylating Drc1 and regulating its association with
Cut5. Sld2 and Sld3 represent the minimal set of S-CDK
substrates required for DNA replication.
Length = 397
Score = 32.1 bits (73), Expect = 0.85
Identities = 36/173 (20%), Positives = 56/173 (32%), Gaps = 28/173 (16%)
Query: 11 KKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPD------ 64
KK S + S K +K S +S+ +P + P SA++S S
Sbjct: 45 KKLLSAKTIEPSPKKRKHSSPDGESQS-TPRKRIPSDVDPYDSPSALRSPSSLKTELGPT 103
Query: 65 -----------DMLQDNGSEDEYVPPKAEVESESEHSSGE--------EELEESVEDPTP 105
D+L + + P + S S+ E L+ ED
Sbjct: 104 PQRDGKVLSLFDLLSSSTPPES--TPSKRKLASSVASATPFSTPSKRRETLDAEDEDRPE 161
Query: 106 SSSEAEVTPMKNGNKRGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPS 158
+E TP+ +G K L + + PS + VS TS S
Sbjct: 162 YGPRSERTPLSSGKKVMLDLFFTPTSWRYSSETPSFLRRSNQDVSATSNPLNS 214
>gnl|CDD|180536 PRK06347, PRK06347, autolysin; Reviewed.
Length = 592
Score = 32.0 bits (72), Expect = 0.96
Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 3/88 (3%)
Query: 72 SEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPT 131
S DE P +S +++ E + E+ T + E + T K K + + QP
Sbjct: 51 SADETAPADEASKSAEANTTKEAPATATPENTTEPTVEPKQTETKEQTK---TPEEKQPA 107
Query: 132 KKPKLTAPSTPSTPSFPVSDTSETTPST 159
K AP+ P+T S P + TS +TP+T
Sbjct: 108 AKQVEKAPAEPATVSNPDNATSSSTPAT 135
>gnl|CDD|218177 pfam04615, Utp14, Utp14 protein. This protein is found to be part
of a large ribonucleoprotein complex containing the U3
snoRNA. Depletion of the Utp proteins impedes production
of the 18S rRNA, indicating that they are part of the
active pre-rRNA processing complex. This large RNP
complex has been termed the small subunit (SSU)
processome.
Length = 728
Score = 32.0 bits (73), Expect = 1.0
Identities = 25/145 (17%), Positives = 46/145 (31%), Gaps = 5/145 (3%)
Query: 3 LDSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSE 62
E E+ + E+ P+ + P E ++ K + + K +SD E
Sbjct: 398 RRELEGEEESDEEENEEPSKKNVGRRKFGPENGEKEAESKKLKKENKNE-FKEKKESDEE 456
Query: 63 PDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDP--TPSSSEAEVTPMKNGNK 120
+ L+D ++ + EEE E E+P +SS + ++ K
Sbjct: 457 EE--LEDEEEAKVEKVANKLLKRSEKAQKEEEEEELDEENPWLKTTSSVGKSAKKQDSKK 514
Query: 121 RGLSSKSGQPTKKPKLTAPSTPSTP 145
+ S K K
Sbjct: 515 KSSSKLDKAANKISKAAVKVKKKKK 539
>gnl|CDD|139494 PRK13335, PRK13335, superantigen-like protein; Reviewed.
Length = 356
Score = 31.6 bits (71), Expect = 1.0
Identities = 27/139 (19%), Positives = 50/139 (35%), Gaps = 5/139 (3%)
Query: 28 TSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESES 87
T A+ + V K P K+ + I + + N ++ + +
Sbjct: 25 TQSVKAEKIQSTKVDKVPTLKAERLAMINITAGANSATTQAANTRQERTPKLEKAPNTNE 84
Query: 88 EHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTK-KPKLTAPSTPSTPS 146
E +S E + P ++ K+ S + + T K K+T P + +TP
Sbjct: 85 EKTSAS--KIEKISQPKQEEQKSLNISATPAPKQEQSQTTTESTTPKTKVTTPPSTNTPQ 142
Query: 147 FPVSDTSET--TPSTSGAQ 163
S S+T +P+ AQ
Sbjct: 143 PMQSTKSDTPQSPTIKQAQ 161
>gnl|CDD|235285 PRK04335, PRK04335, cell division protein ZipA; Provisional.
Length = 313
Score = 31.7 bits (72), Expect = 1.1
Identities = 20/108 (18%), Positives = 43/108 (39%), Gaps = 5/108 (4%)
Query: 9 PEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQ 68
P K D +S + + +++P EDD + ++ R++ +++ D +
Sbjct: 39 PLGKLDVDSDDEQPAPERGFAQAP---EDDFEIIRKERKEPDFGRENSFHDPLIDDPLFG 95
Query: 69 DNGSEDEYVPPKAEVE--SESEHSSGEEELEESVEDPTPSSSEAEVTP 114
E+E + E +++ E++E VE+P E P
Sbjct: 96 GELEEEEDKFEQEEAPIPVQAQSQPQPEKVEPQVEEPRDEEVLEEPEP 143
>gnl|CDD|217393 pfam03154, Atrophin-1, Atrophin-1 family. Atrophin-1 is the
protein product of the dentatorubral-pallidoluysian
atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive
neurodegenerative disorder. It is caused by the
expansion of a CAG repeat in the DRPLA gene on
chromosome 12p. This results in an extended
polyglutamine region in atrophin-1, that is thought to
confer toxicity to the protein, possibly through
altering its interactions with other proteins. The
expansion of a CAG repeat is also the underlying defect
in six other neurodegenerative disorders, including
Huntington's disease. One interaction of expanded
polyglutamine repeats that is thought to be pathogenic
is that with the short glutamine repeat in the
transcriptional coactivator CREB binding protein, CBP.
This interaction draws CBP away from its usual nuclear
location to the expanded polyglutamine repeat protein
aggregates that are characteristic of the polyglutamine
neurodegenerative disorders. This interferes with
CBP-mediated transcription and causes cytotoxicity.
Length = 979
Score = 32.0 bits (72), Expect = 1.1
Identities = 33/172 (19%), Positives = 62/172 (36%), Gaps = 38/172 (22%)
Query: 4 DSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQS---- 59
+S + P KK E+++P S K+ + PA ++ P R +AK+ K+ S
Sbjct: 60 ESTKKPNKKIKEEATSPLKS-TKRQREKPASDTEE------PERVTAKKSKTQELSRPNS 112
Query: 60 ------------------------DSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEE 95
S+P D+ QDN S +P + ES+S+ S+ ++
Sbjct: 113 PSEGEGEGEGEGESSDSRSVNEEGSSDPKDIDQDNRSSSPSIPSPQDNESDSDSSAQQQL 172
Query: 96 LEES---VEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPKLTAPSTPST 144
L+ P ++ A P + + + + +P
Sbjct: 173 LQPQGPPSIQVPPGAALAPSAPPPTPSAQAVPPQGSPIAAQPAPQPQQPSPL 224
Score = 30.4 bits (68), Expect = 3.2
Identities = 42/159 (26%), Positives = 55/159 (34%), Gaps = 20/159 (12%)
Query: 13 GDSESSTPASSKGKKTSKSPAKSEDDSPV--TKRPRRKSAK------RVKSAIQSDSEPD 64
S SS + ++ K K E SP+ TKR R K A RV + E
Sbjct: 49 AASTSSNDSKAESTKKPNKKIKEEATSPLKSTKRQREKPASDTEEPERVTAKKSKTQELS 108
Query: 65 DMLQDNGSEDEYVPPKAEVESESEHS-SGEEELEESVED---PTPSSSEAEVTPMKNGNK 120
+ E E E E ES S S EE +D SSS + +P N +
Sbjct: 109 RPNSPSEGEGE-----GEGEGESSDSRSVNEEGSSDPKDIDQDNRSSSPSIPSPQDNESD 163
Query: 121 RGLSSKS--GQPTKKPKLTAPS-TPSTPSFPVSDTSETT 156
S++ QP P + P PS P S
Sbjct: 164 SDSSAQQQLLQPQGPPSIQVPPGAALAPSAPPPTPSAQA 202
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 31.8 bits (72), Expect = 1.2
Identities = 23/155 (14%), Positives = 45/155 (29%), Gaps = 29/155 (18%)
Query: 8 SPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDML 67
P + + P + ++ ++ S +RPRR++A+ ++ S ++P
Sbjct: 2646 VPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPP--- 2702
Query: 68 QDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSSKS 127
PP E P S + P ++ +
Sbjct: 2703 ----------PPPPTPEPA----------------PHALVSATPLPPGPAAARQASPALP 2736
Query: 128 GQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGA 162
P P+TP P+ P + P
Sbjct: 2737 AAPAPPAVPAGPATPGGPARPARPPTTAGPPAPAP 2771
Score = 30.7 bits (69), Expect = 2.9
Identities = 22/152 (14%), Positives = 38/152 (25%), Gaps = 7/152 (4%)
Query: 8 SPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDML 67
SP P S ++ P +RPR A S +
Sbjct: 2615 SPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAA 2674
Query: 68 QDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSSKS 127
Q + A S S + +P P + + +
Sbjct: 2675 QASSPPQRPRRRAARPTVGSLTSLADPPPPPPTPEPAP-------HALVSATPLPPGPAA 2727
Query: 128 GQPTKKPKLTAPSTPSTPSFPVSDTSETTPST 159
+ AP+ P+ P+ P + P+
Sbjct: 2728 ARQASPALPAAPAPPAVPAGPATPGGPARPAR 2759
>gnl|CDD|148635 pfam07139, DUF1387, Protein of unknown function (DUF1387). This
family represents a conserved region approximately 300
residues long within a number of hypothetical proteins
of unknown function that seem to be restricted to
mammals.
Length = 301
Score = 31.5 bits (71), Expect = 1.3
Identities = 25/139 (17%), Positives = 50/139 (35%)
Query: 26 KKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVES 85
KK K +K + ++P + ++ ++A + + + NGS D+ + E
Sbjct: 7 KKNKKKKSKPKPEAPAKSASKEETTPEEQAAPGDEKDEVNGFHANGSADDTESVDSLSEG 66
Query: 86 ESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPKLTAPSTPSTP 145
S E E D PS S + + + + S + KP ++ +
Sbjct: 67 LDSASLDAREPEAVTLDAPPSPSSSLTNGLSDLQSKLELQSSPHSSAKPHPSSDQHKNAK 126
Query: 146 SFPVSDTSETTPSTSGAQD 164
+ + TP+ S D
Sbjct: 127 KYVSKPSQPVTPNNSAHHD 145
>gnl|CDD|221179 pfam11711, Tim54, Inner membrane protein import complex subunit
Tim54. Mitochondrial function depends on the import of
hundreds of different proteins synthesised in the
cytosol. Protein import is a multi-step pathway which
includes the binding of precursor proteins to surface
receptors, translocation of the precursor across one or
both mitochondrial membranes, and folding and assembly
of the imported protein inside the mitochondrion. Most
precursor proteins carry amino-terminal targeting
signals, called pre-sequences, and are imported into
mitochondria via import complexes located in both the
outer and the inner membrane (IM). The IM complex, TIM,
is made up of at least two proteins which mediate
translocation of proteins into the matrix by removing
their signal peptide and another pair of proteins, Tim54
and Tim22, that insert the polytopic proteins, that
carry internal targetting information, into the inner
membrane.
Length = 377
Score = 31.2 bits (71), Expect = 1.3
Identities = 15/82 (18%), Positives = 25/82 (30%), Gaps = 9/82 (10%)
Query: 77 VPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPKL 136
PP+ + E ++ E E+E + +P+ E + KP +
Sbjct: 196 DPPEPPEPTVDE-AAPETEVEATPAAESPAEPAEETAETTPEETEDAPEEENNKPVKPPV 254
Query: 137 TAP--------STPSTPSFPVS 150
P S P P P
Sbjct: 255 PKPYISPDEYPSAPLPPELPQL 276
>gnl|CDD|185628 PTZ00449, PTZ00449, 104 kDa microneme/rhoptry antigen; Provisional.
Length = 943
Score = 31.6 bits (71), Expect = 1.6
Identities = 27/134 (20%), Positives = 46/134 (34%), Gaps = 17/134 (12%)
Query: 43 KRPRRKSAKRVKSAIQSDSE---------------PDDMLQDNGSEDEYVPPKAEVESES 87
K+ +KS K++ + DS+ P G E E+ K E +
Sbjct: 486 KKLIKKSKKKLAPIEEEDSDKHDEPPEGPEASGLPPKAPGDKEGEEGEHEDSKESDEPKE 545
Query: 88 EHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPKL-TAPSTPSTPS 146
GE + E + P P + E + + + +K+ K + K P+ P P +
Sbjct: 546 GGKPGETKEGEVGKKPGP-AKEHKPSKIPTLSKKPEFPKDPKHPKDPEEPKKPKRPRSAQ 604
Query: 147 FPVSDTSETTPSTS 160
P S P
Sbjct: 605 RPTRPKSPKLPELL 618
Score = 30.8 bits (69), Expect = 2.2
Identities = 29/152 (19%), Positives = 57/152 (37%), Gaps = 16/152 (10%)
Query: 11 KKGDSESSTPASSKGKKTSKSPAKSEDDSPVT----KRPRRKSAKRVKSAIQSDSEPDDM 66
K+ D + T + K SP++ ED P + R + S +S+ +
Sbjct: 778 KEEDIHAETGEPDEAMKRPDSPSEHEDKPPGDHPSLPKKRHRLDGLALSTTDLESDAGRI 837
Query: 67 LQD----------NGSEDEY--VPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTP 114
+D + S D+ V E+ +E+ +++ E+ ++ T E +
Sbjct: 838 AKDASGKIVKLKRSKSFDDLTTVEEAEEMGAEARKIVVDDDGTEADDEDTHPPEEKHKSE 897
Query: 115 MKNGNKRGLSSKSGQPTKKPKLTAPSTPSTPS 146
++ SK +P+K K P + PS
Sbjct: 898 VRRRRPPKKPSKPKKPSKPKKPKKPDSAFIPS 929
Score = 30.8 bits (69), Expect = 2.2
Identities = 28/163 (17%), Positives = 50/163 (30%), Gaps = 7/163 (4%)
Query: 4 DSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEP 63
D K + + + P S++ KSP K + + K P+R + + P
Sbjct: 584 DPKHPKDPEEPKKPKRPRSAQRPTRPKSP-KLPELLDIPKSPKRPESPKSPKRPPPPQRP 642
Query: 64 DDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGN---- 119
+ G + P + +E+ + D S E + T + + +
Sbjct: 643 SSPERPEGPKIIKSPKPPKSPKPPFDPKFKEKFYDDYLDAAAKSKETKTTVVLDESFESI 702
Query: 120 -KRGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSE-TTPSTS 160
K L G P P+ P P FP +
Sbjct: 703 LKETLPETPGTPFTTPRPLPPKLPRDEEFPFEPIGDPDAEQPD 745
Score = 30.8 bits (69), Expect = 2.3
Identities = 32/155 (20%), Positives = 55/155 (35%), Gaps = 30/155 (19%)
Query: 4 DSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSP-----VTKRP----RRKSAKRVK 54
DSKES E K E P +K + K P +++ P ++K+P K K +
Sbjct: 536 DSKESDEPK---EGGKPGETKEGEVGKKPGPAKEHKPSKIPTLSKKPEFPKDPKHPKDPE 592
Query: 55 SAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDP-TPSSSEAEVT 113
+ + +S ++ +S + P +P S +
Sbjct: 593 EPKKPKRP--------------RSAQRPTRPKSPKLPELLDIPKSPKRPESPKSPKRPPP 638
Query: 114 PMKNGN-KRGLSSKSGQPTKKPKLTAPSTPSTPSF 147
P + + +R K + K PK +P P P F
Sbjct: 639 PQRPSSPERPEGPKIIKSPKPPK--SPKPPFDPKF 671
>gnl|CDD|215018 smart01087, COG6, Conserved oligomeric complex COG6. COG6 is a
component of the conserved oligomeric golgi complex,
which is composed of eight different subunits and is
required for normal golgi morphology and localisation.
Length = 598
Score = 31.1 bits (71), Expect = 1.6
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 13/64 (20%)
Query: 493 MEARHNLR-----------QLFIHKFASLVKSGEKV--DVEELQKALESVKSFESQTKKD 539
+EAR NLR F+ +F + + +++ DV++L + +S+K + K
Sbjct: 2 LEARRNLRSDLEKRLLKINGEFLSEFKPVAEQLQRLSEDVQKLNNSCDSMKDQLNTAKNQ 61
Query: 540 LEDL 543
+DL
Sbjct: 62 TQDL 65
>gnl|CDD|220710 pfam10351, Apt1, Golgi-body localisation protein domain. This is
the C-terminus of a family of proteins conserved from
plants to humans. The plant members are localised to the
Golgi proteins and appear to regulate membrane
trafficking, as they are required for rapid vesicle
accumulation at the tip of the pollen tube. The
C-terminus probably contains the Golgi localisation
signal and it is well-conserved.
Length = 451
Score = 31.1 bits (71), Expect = 1.7
Identities = 15/66 (22%), Positives = 28/66 (42%), Gaps = 4/66 (6%)
Query: 3 LDSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSE 62
S + + S+ +SS +S +KS D S + +R S K KS + +
Sbjct: 318 SSSSSGSRRSSSTSRSSSSSSSLLSSSSILSKSSDKS----KDKRFSLKLSKSEKEESDD 373
Query: 63 PDDMLQ 68
++M+
Sbjct: 374 LEEMIS 379
>gnl|CDD|220402 pfam09787, Golgin_A5, Golgin subfamily A member 5. Members of this
family of proteins are involved in maintaining Golgi
structure. They stimulate the formation of Golgi stacks
and ribbons, and are involved in intra-Golgi retrograde
transport. Two main interactions have been
characterized: one with RAB1A that has been activated by
GTP-binding and another with isoform CASP of CUTL1.
Length = 509
Score = 31.0 bits (70), Expect = 1.9
Identities = 26/113 (23%), Positives = 45/113 (39%), Gaps = 4/113 (3%)
Query: 16 ESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDE 75
SS A S+ +K + S SP +K+ +++ + S + + + EDE
Sbjct: 51 ASSNKARSRSEKWNPDQPGSRVSSPSSKKDG--TSRSLSSQVDDLASAVSSQSSSDLEDE 108
Query: 76 YVPPKAEV-ESESEHSSGEEELEE-SVEDPTPSSSEAEVTPMKNGNKRGLSSK 126
K + E+ E + ELE+ E S E + ++ G R L K
Sbjct: 109 LAALKIRLQEAAQELRELKSELEDLRSERSRDLSDEESIKRLQRGAVRSLQDK 161
>gnl|CDD|227805 COG5518, COG5518, Bacteriophage capsid portal protein [General
function prediction only].
Length = 492
Score = 31.1 bits (70), Expect = 1.9
Identities = 20/64 (31%), Positives = 28/64 (43%)
Query: 499 LRQLFIHKFASLVKSGEKVDVEELQKALESVKSFESQTKKDLEDLPGGVAGAGTEWWPSP 558
L L I + +K + +D E + AL + + + DL DL G V G E WP
Sbjct: 403 LEVLPIQERRLALKGPDWIDPEVIAFALYPFITAGAVSPNDLRDLAGRVLGKTLEEWPEE 462
Query: 559 SNDP 562
N P
Sbjct: 463 YNRP 466
>gnl|CDD|227931 COG5644, COG5644, Uncharacterized conserved protein [Function
unknown].
Length = 869
Score = 31.2 bits (70), Expect = 2.0
Identities = 14/58 (24%), Positives = 30/58 (51%), Gaps = 8/58 (13%)
Query: 60 DSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKN 117
++ +++L+ + S +SESE S E E+E S D +S++++ ++N
Sbjct: 147 ATDKENLLESDASSSN--------DSESEESDSESEIESSDSDHDDENSDSKLDNLRN 196
>gnl|CDD|234428 TIGR03979, His_Ser_Rich, His-Xaa-Ser repeat protein HxsA. Members
of this protein share two defining regions. One is a
histidine/serine-rich cluster, typically
H-R-S-H-S-S-H-R-S-H-S-S-H. Members are found always in
the context of a pair of radical SAM proteins, HxsB and
HxsC, and a fourth protein HxsD. The system is predicted
to perform peptide modifications, likely in the
His-Xaa-Ser region, to produce some uncharacterized
natural product.
Length = 186
Score = 30.2 bits (68), Expect = 2.1
Identities = 10/40 (25%), Positives = 14/40 (35%), Gaps = 2/40 (5%)
Query: 121 RGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTS 160
G +S P P + S S P T+ P +S
Sbjct: 80 SGDTSTYSYPVPSPSYSPSPGSSIQSLPS--TTGVRPQSS 117
>gnl|CDD|227578 COG5253, MSS4, Phosphatidylinositol-4-phosphate 5-kinase [Signal
transduction mechanisms].
Length = 612
Score = 30.7 bits (69), Expect = 2.3
Identities = 32/169 (18%), Positives = 58/169 (34%), Gaps = 13/169 (7%)
Query: 3 LDSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSA------ 56
+ E S+ T + SK + + R+ A R++++
Sbjct: 44 ANGNEYSPNNKVSKKDTFSDQLHDALSKEFTLERERDRLQLNKRKYQAIRLQTSTPIVEI 103
Query: 57 ---IQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHS-SGEEELEESVEDPTPSSSEAEV 112
+ +P + + +G+ K EHS S + D P SS ++
Sbjct: 104 FKNNKDAVDPPNHTRSSGNNLSNANVKTLSAPVGEHSRSNNPPNLDQNLDTEPESSISQW 163
Query: 113 TPMKNGNKRGLSSKSGQPTKKPKLTAPSTPSTPS-FPVSDTSETTPSTS 160
++ N G + S QP++KP P + S S P S S +
Sbjct: 164 GELQL-NPSGKTLSS-QPSRKPTSENPKSESDNSKLPTSVNSPLPDKSL 210
>gnl|CDD|191309 pfam05597, Phasin, Poly(hydroxyalcanoate) granule associated
protein (phasin). Polyhydroxyalkanoates (PHAs) are
storage polyesters synthesised by various bacteria as
intracellular carbon and energy reserve material. PHAs
are accumulated as water-insoluble inclusions within the
cells. This family consists of the phasins PhaF and PhaI
which act as a transcriptional regulator of PHA
biosynthesis genes. PhaF has been proposed to repress
expression of the phaC1 gene and the phaIF operon.
Length = 132
Score = 29.6 bits (67), Expect = 2.3
Identities = 11/43 (25%), Positives = 21/43 (48%)
Query: 507 FASLVKSGEKVDVEELQKALESVKSFESQTKKDLEDLPGGVAG 549
F +LVK GE+++ + A E V++ K + ++ G
Sbjct: 41 FEALVKEGEELEKRTRKLAEEQVEAVRESVKSRVSEVKDKAEG 83
>gnl|CDD|218370 pfam04997, RNA_pol_Rpb1_1, RNA polymerase Rpb1, domain 1. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 1, represents the clamp domain, which a
mobile domain involved in positioning the DNA,
maintenance of the transcription bubble and positioning
of the nascent RNA strand.
Length = 330
Score = 30.3 bits (69), Expect = 2.4
Identities = 19/91 (20%), Positives = 38/91 (41%), Gaps = 10/91 (10%)
Query: 326 KEIQTYLRTQCAHFGCTVIYSEAQKKQKKYVLEVPSKYASKAKSNHQRVAT--KKKNVEN 383
K+I + LR C +++ +E+ K V+ P SK + +++ KKK++ +
Sbjct: 87 KKILSILRCVC-KLCSSLLLNESVKYFFLKVVIDPKGKNSKKR--LKKINNLCKKKSICS 143
Query: 384 YVTPECRGTGTNDGC-----VIARVTLEKFL 409
+ G +GC I++ E
Sbjct: 144 KCGEDNGGLKAFEGCGKYQPKISKDGAEAIK 174
>gnl|CDD|233044 TIGR00600, rad2, DNA excision repair protein (rad2). All proteins
in this family for which functions are known are flap
endonucleases that generate the 3' incision next to DNA
damage as part of nucleotide excision repair. This
family is related to many other flap endonuclease
families including the fen1 family. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University) [DNA metabolism, DNA
replication, recombination, and repair].
Length = 1034
Score = 31.0 bits (70), Expect = 2.4
Identities = 30/160 (18%), Positives = 52/160 (32%), Gaps = 12/160 (7%)
Query: 23 SKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQD-NGSEDEYVPPKA 81
+ K + S DD P +K+ + S I+ + + D L G +
Sbjct: 402 ALDDDEDKKVSASSDDQ---ASPSKKTKMLLISRIEVEDDDLDYLDQGEGIPLMAALQLS 458
Query: 82 EVESESEH---SSGEEELEESVEDPTPSSSEAEVTPMKNGNK-----RGLSSKSGQPTKK 133
V S+ E + E+ S + P + ++ + N + L KS ++
Sbjct: 459 SVNSKPEAVASTKIAREVTSSGHEAVPKAVQSLLLGATNDSPIPSEFTILDRKSELSIER 518
Query: 134 PKLTAPSTPSTPSFPVSDTSETTPSTSGAQDWSHNHYQFL 173
S PS + T T Q S + QF
Sbjct: 519 TVKPVSSEFGLPSQREDKLAIPTEGTQNLQGISDHPEQFE 558
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 30.1 bits (68), Expect = 2.5
Identities = 17/90 (18%), Positives = 31/90 (34%), Gaps = 12/90 (13%)
Query: 7 ESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDM 66
KK + + A + A +E D + K + + A SD++ D
Sbjct: 69 AHKSKKENKLAIEDADKS----TNLDASNEGDEDDDEEDEIKRKRIEEDARNSDADDSDS 124
Query: 67 LQDNGSEDEYVPPKAEVESESEHSSGEEEL 96
D+ S D+ +S+ + S E
Sbjct: 125 SSDSDSSDD--------DSDDDDSEDETAA 146
>gnl|CDD|221825 pfam12877, DUF3827, Domain of unknown function (DUF3827). This
family contains the human KIAA1549 protein which has
been found to be fused fused to BRAF gene in many cases
of pilocytic astrocytomas. The fusion is due mainly to a
tandem duplication of 2 Mb at 7q34. Although nothing is
known about the function of KIAA1549 protein, the BRAF
protein is a well characterized oncoprotein. It is a
serine/threonine protein kinase which is implicated in
MAP/ERK signalling, a critical pathway for the
regulation of cell division, differentiation and
secretion.
Length = 684
Score = 30.3 bits (68), Expect = 3.4
Identities = 28/156 (17%), Positives = 54/156 (34%), Gaps = 22/156 (14%)
Query: 8 SPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDML 67
+P+ K + S+ + + S S SE S ++ R R+ + R + S +
Sbjct: 364 TPKSKSSQDGSSNKKRRRGRKSPSDGDSEGSSVISNRSSREKSGRPSTT-PSVTAQQKPT 422
Query: 68 QDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSSKS 127
++ G + PP + + SS + E V+ + SS+ S K
Sbjct: 423 KEEGRKKP-APPSGT---DEQLSSA--SIFEHVDRLSRPSSDP---------YDRSSGKI 467
Query: 128 GQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGAQ 163
+P P+ P P + S + +
Sbjct: 468 QLIAMQP------MPAPPVPPRFEPSRDDRAAENGK 497
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 30.4 bits (68), Expect = 3.7
Identities = 25/107 (23%), Positives = 42/107 (39%), Gaps = 6/107 (5%)
Query: 1 MYLDSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSD 60
+ LD KE K DS+ + +K A +E D P+ + + IQ D
Sbjct: 3993 LKLDEKEGDVSK-DSDLEDMDMEAADE-NKEEADAEKDEPMQDEDPLEENNTLDEDIQQD 4050
Query: 61 SEPDDMLQDNGSEDEYVPPKAEVESESEHSSG---EEELEESVEDPT 104
+ D+ +D+ +E + E+E G +EELE+
Sbjct: 4051 -DFSDLAEDDEKMNEDGFEENVQENEESTEDGVKSDEELEQGEVPED 4096
>gnl|CDD|234706 PRK00269, zipA, cell division protein ZipA; Reviewed.
Length = 293
Score = 29.7 bits (67), Expect = 4.1
Identities = 26/106 (24%), Positives = 40/106 (37%), Gaps = 17/106 (16%)
Query: 14 DSESSTP---ASSKGKKTSKSPAKSEDDSP-VTKRPR-----RKSAKRVKSAIQSDSEPD 64
D E + ++ T K P E D P ++ RPR K+AK+ K S+ +
Sbjct: 48 DEEEGSAELLGPARVLDTHKEPQLDEHDLPSMSARPRERRRDTKTAKQQKRGRGSEPQQG 107
Query: 65 DMLQDNGSEDEYVPP-----KAEVESESEHSSGEEELEESVEDPTP 105
D+ N DE P + + S G E E ++ P
Sbjct: 108 DL---NLDLDEVEPALFSDRDDDFTPDKRKSKGREPRIEPPKELPP 150
>gnl|CDD|215641 PLN03237, PLN03237, DNA topoisomerase 2; Provisional.
Length = 1465
Score = 30.2 bits (68), Expect = 4.4
Identities = 21/121 (17%), Positives = 39/121 (32%), Gaps = 7/121 (5%)
Query: 20 PASSKGKKTSKSPAKSEDD-SPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVP 78
A KK + PA + + +++ V+S + +E + G E
Sbjct: 1326 LAERLKKKGGRKPAAANKKAAKPPAAAKKRGPATVQSGQKLLTEMLKPAEAIGISPEKKV 1385
Query: 79 PKAEVESESEHSS------GEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTK 132
K ++ S + ES E+ + SSS + + R + Q T
Sbjct: 1386 RKMRASPFNKKSGSVLGRAATNKETESSENVSGSSSSEKDEIDVSAKPRPQRANRKQTTY 1445
Query: 133 K 133
Sbjct: 1446 V 1446
Score = 29.4 bits (66), Expect = 6.2
Identities = 19/67 (28%), Positives = 25/67 (37%), Gaps = 4/67 (5%)
Query: 8 SPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRP---RRKSAKRVKSAIQSDSEPD 64
S + + T SS+ S S K E D RP RK V S +S+S D
Sbjct: 1399 SVLGRAATNKET-ESSENVSGSSSSEKDEIDVSAKPRPQRANRKQTTYVLSDSESESADD 1457
Query: 65 DMLQDNG 71
D+
Sbjct: 1458 SDFDDDE 1464
>gnl|CDD|176015 cd04050, C2B_Synaptotagmin-like, C2 domain second repeat present
in Synaptotagmin-like proteins. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Previously all synaptotagmins
were thought to be calcium sensors in the regulation of
neurotransmitter release and hormone secretion, but it
has been shown that not all of them bind calcium. Of
the 17 identified synaptotagmins only 8 bind calcium
(1-3, 5-7, 9, 10). The function of the two C2 domains
that bind calcium are: regulating the fusion step of
synaptic vesicle exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
C2 domains fold into an 8-standed beta-sandwich that
can adopt 2 structural arrangements: Type I and Type
II, distinguished by a circular permutation involving
their N- and C-terminal beta strands. Many C2 domains
are Ca2+-dependent membrane-targeting modules that bind
a wide variety of substances including bind
phospholipids, inositol polyphosphates, and
intracellular proteins. Most C2 domain proteins are
either signal transduction enzymes that contain a
single C2 domain, such as protein kinase C, or membrane
trafficking proteins which contain at least two C2
domains, such as synaptotagmin 1. However, there are a
few exceptions to this including RIM isoforms and some
splice variants of piccolo/aczonin and intersectin
which only have a single C2 domain. C2 domains with a
calcium binding region have negatively charged
residues, primarily aspartates, that serve as ligands
for calcium ions. This cd contains the second C2
repeat, C2B, and has a type-I topology.
Length = 105
Score = 27.9 bits (63), Expect = 4.5
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 2/43 (4%)
Query: 1 MYLDSKES-PEKKGDSESSTPAS-SKGKKTSKSPAKSEDDSPV 41
+YLDS ++ P K E S + GK T KS K ++PV
Sbjct: 4 VYLDSAKNLPLAKSTKEPSPYVELTVGKTTQKSKVKERTNNPV 46
>gnl|CDD|218737 pfam05764, YL1, YL1 nuclear protein. The proteins in this family
are designated YL1. These proteins have been shown to be
DNA-binding and may be a transcription factor.
Length = 238
Score = 29.3 bits (66), Expect = 4.6
Identities = 25/129 (19%), Positives = 45/129 (34%), Gaps = 11/129 (8%)
Query: 41 VTKRPRRKSA-KRVKSAIQSDSEPDDMLQDNGS------EDEYV----PPKAEVESESEH 89
R RR +A R+K ++ + E D+ ++E+ + EV+S+ +
Sbjct: 1 AATRARRSNAGNRMKKLLEEELEEDEFFWTYLLFEEEEDDEEFEIEEEEEEEEVDSDFDD 60
Query: 90 SSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPKLTAPSTPSTPSFPV 149
S +E + E+ E K K + + KK TA +P +
Sbjct: 61 SEDDEPESDDEEEGEKELQREERLKKKKRVKTKAYKEPTKKKKKKDPTAAKSPKAAAPRP 120
Query: 150 SDTSETTPS 158
SE
Sbjct: 121 KKKSERISW 129
>gnl|CDD|220271 pfam09507, CDC27, DNA polymerase subunit Cdc27. This protein forms
the C subunit of DNA polymerase delta. It carries the
essential residues for binding to the Pol1 subunit of
polymerase alpha, from residues 293-332, which are
characterized by the motif D--G--VT, referred to as the
DPIM motif. The first 160 residues of the protein form
the minimal domain for binding to the B subunit, Cdc1,
of polymerase delta, the final 10 C-terminal residues,
362-372, being the DNA sliding clamp, PCNA, binding
motif.
Length = 427
Score = 29.4 bits (66), Expect = 5.6
Identities = 23/119 (19%), Positives = 43/119 (36%), Gaps = 19/119 (15%)
Query: 4 DSKESPEKKGDSESSTPASS--------KGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKS 55
K + K+ + S SS K +K S + +++S R
Sbjct: 201 SVKAASLKRNPPKKSNIMSSFFKKKTKEKKEKKEASESTVKEESEEESGKRDV------- 253
Query: 56 AIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGE--EELEESVEDPTPSSSEAEV 112
++ +S L ++ EDE P + S+SE + E +E + ++ E E
Sbjct: 254 ILEDESAEPTGLDEDEDEDE--PKPSGERSDSEEETEEKEKEKRKRLKKMMEDEDEDEE 310
>gnl|CDD|220684 pfam10310, DUF2413, Protein of unknown function (DUF2413). This is
a family of proteins conserved in fungi. The function is
not known.
Length = 436
Score = 29.4 bits (66), Expect = 6.2
Identities = 23/88 (26%), Positives = 31/88 (35%), Gaps = 8/88 (9%)
Query: 3 LDSKESPEKKGDSESSTPASSKG-----KKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAI 57
LD E EK + AS G KK+SK S S RKSA +S
Sbjct: 38 LDELEQSEKAKPPKKPKEASRPGTPRNPKKSSKPTESSAASSEEKPAKPRKSA---ESTR 94
Query: 58 QSDSEPDDMLQDNGSEDEYVPPKAEVES 85
S + ++ E+E + S
Sbjct: 95 SSHPKSKAPSTESEEEEEPEETPDPIAS 122
>gnl|CDD|113514 pfam04747, DUF612, Protein of unknown function, DUF612. This
family includes several uncharacterized proteins from
Caenorhabditis elegans.
Length = 517
Score = 29.3 bits (64), Expect = 6.4
Identities = 43/165 (26%), Positives = 70/165 (42%), Gaps = 20/165 (12%)
Query: 6 KESPEKKGDSESSTPASSKGKKTSK--SPAKSEDDSPVTKRPRRKSAKRV---KSAIQSD 60
K EKK + + K +KT K +PA E++ V K +SA K+ +
Sbjct: 142 KLQAEKKKEKAVKAEKAEKAEKTKKASTPAPVEEEIVVKKVANDRSAAPAPEPKTPTNTP 201
Query: 61 SEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSE--AEVTPMKNG 118
+EP + +Q+ + K + +SESE ++ +E+ VE P + E + P +
Sbjct: 202 AEPAEQVQEITGKKN---KKNKKKSESEATAAPASVEQVVEQPKVVTEEPHQQAAPQEKK 258
Query: 119 NKRGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGAQ 163
NK+ K K + + P+ PV ETTP S Q
Sbjct: 259 NKK----------NKRKSESENVPAASETPVEPVVETTPPASENQ 293
Score = 28.9 bits (63), Expect = 9.4
Identities = 29/140 (20%), Positives = 57/140 (40%), Gaps = 2/140 (1%)
Query: 6 KESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDD 65
K KK +T A + ++ + P ++ P+ K K+ K +S++ P
Sbjct: 215 KNKKNKKKSESEATAAPASVEQVVEQPKVVTEEPHQQAAPQEKKNKKNKRKSESENVPAA 274
Query: 66 MLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSS 125
E PP +E + +++ + E E+ VE+P + + P + N L
Sbjct: 275 SETPVEPVVETTPPASENQKKNKKDKKKSESEKVVEEPVQAEAPKSKKPTADDNMDFLDF 334
Query: 126 KSGQPTKKPKLTAPSTPSTP 145
+ + ++PK TP+ P
Sbjct: 335 VTAK--EEPKDEPAETPAAP 352
>gnl|CDD|223068 PHA03384, PHA03384, early DNA-binding protein E2A; Provisional.
Length = 445
Score = 29.3 bits (66), Expect = 6.4
Identities = 19/90 (21%), Positives = 31/90 (34%), Gaps = 7/90 (7%)
Query: 25 GKKTSKSPAKSEDDSPVT----KRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPK 80
G+ +S S DDSP P++K +RV + + E + + G PP
Sbjct: 3 GRGSSSDSPYSSDDSPSLEPPELPPKKKGRRRVSPVEEEEEEEEAEVVAVGFSY---PPV 59
Query: 81 AEVESESEHSSGEEELEESVEDPTPSSSEA 110
+ EE + S+ A
Sbjct: 60 RISRGKDGKRPVRPLKEEKDSEKKASTEAA 89
>gnl|CDD|221745 pfam12737, Mating_C, C-terminal domain of homeodomain 1. Mating in
fungi is controlled by the loci that determine the
mating type of an individual, and only individuals with
differing mating types can mate. Basidiomycete fungi
have evolved a unique mating system, termed tetrapolar
or bifactorial incompatibility, in which mating type is
determined by two unlinked loci; compatibility at both
loci is required for mating to occur. The multi-allelic
tetrapolar mating system is considered to be a novel
innovation that could have only evolved once, and is
thus unique to the mushroom fungi. This domain is
C-terminal to the homeodomain transcription factor
region.
Length = 418
Score = 29.0 bits (65), Expect = 6.8
Identities = 34/151 (22%), Positives = 53/151 (35%), Gaps = 20/151 (13%)
Query: 8 SPEKKGDSESSTPASSKGKKTSKSPAKSEDD---SPVTKRPRRKSAKRVKSAIQSDSEPD 64
SP S AS + K +S + S+D+ +KRPR +I S S P
Sbjct: 87 SPSPSVLDLSPVLASPQTGKRRRSSSPSDDEDEAERPSKRPRS-------DSISSSSSPA 139
Query: 65 DMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLS 124
E P A + E +S S+ P + T KR LS
Sbjct: 140 KP-----PEACLPSPAASTQDELSEASAAPLPTPSLSPPHTPTD----TAPSGKRKRRLS 190
Query: 125 SKSGQP-TKKPKLTAPSTPSTPSFPVSDTSE 154
P K+P+ ++ + P+ T++
Sbjct: 191 DGFQLPAPKRPQTSSRPQTVSDPLPLHATTD 221
>gnl|CDD|239091 cd02407, PTH2_family, Peptidyl-tRNA hydrolase, type 2 (PTH2)_like .
Peptidyl-tRNA hydrolase activity releases tRNA from the
premature translation termination product peptidyl-tRNA.
Two structurally different enzymes have been reported to
encode such activity, Pth present in bacteria and
eukaryotes and Pth2 present in archaea and eukaryotes.
Length = 115
Score = 27.9 bits (63), Expect = 7.0
Identities = 19/54 (35%), Positives = 22/54 (40%), Gaps = 18/54 (33%)
Query: 334 TQCAHFGCTVIYSEAQKK------------QKKYVLEVPS-----KYASKAKSN 370
QCAH Y +A K QKK VL+VPS + A KAK
Sbjct: 20 AQCAH-AALAAYKKAMKDPPTLLRAWELEGQKKVVLKVPSEEELLELAKKAKEL 72
>gnl|CDD|233045 TIGR00601, rad23, UV excision repair protein Rad23. All proteins
in this family for which functions are known are
components of a multiprotein complex used for targeting
nucleotide excision repair to specific parts of the
genome. In humans, Rad23 complexes with the XPC protein.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 378
Score = 29.1 bits (65), Expect = 7.0
Identities = 11/42 (26%), Positives = 14/42 (33%)
Query: 118 GNKRGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPST 159
+ + K P P TPS P+ P S S S
Sbjct: 75 SKPKTGTGKVAPPAATPTSAPTPTPSPPASPASGMSAAPASA 116
>gnl|CDD|227925 COG5638, COG5638, Uncharacterized conserved protein [Function
unknown].
Length = 622
Score = 29.4 bits (65), Expect = 7.0
Identities = 20/60 (33%), Positives = 25/60 (41%), Gaps = 11/60 (18%)
Query: 74 DEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKK 133
DEY P + E + SS E EES E+ SE K G + G PTK+
Sbjct: 100 DEYDPARGEGIISTSESSDESR-EESEEEKANEISE----------KAGAVPEEGNPTKR 148
>gnl|CDD|234698 PRK00236, xerC, site-specific tyrosine recombinase XerC; Reviewed.
Length = 297
Score = 29.0 bits (66), Expect = 7.1
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 170 YQFLHPDHILDADR----RSPKHPDYNPKTLYV 198
Y++L +L A+ R+PK P PK L V
Sbjct: 86 YRWLVRRGLLKANPAAGLRAPKIPKRLPKPLDV 118
>gnl|CDD|200550 cd10924, CE4_COG4878, Putative NodB-like catalytic domain of
uncharacterized proteins found in bacteria. The family
corresponds to a group of uncharacterized bacterial
proteins with high sequence similarity to the catalytic
domain of the six-stranded barrel rhizobial NodB-like
proteins, which remove N-linked or O-linked acetyl
groups from cell wall polysaccharides and belong to the
larger carbohydrate esterase 4 (CE4) superfamily.
Length = 273
Score = 28.8 bits (65), Expect = 7.1
Identities = 10/19 (52%), Positives = 13/19 (68%), Gaps = 4/19 (21%)
Query: 165 WSHNHYQFLHPDHILDADR 183
SH F+HPD +LDA+R
Sbjct: 228 VSH----FVHPDDVLDAER 242
>gnl|CDD|237284 PRK13108, PRK13108, prolipoprotein diacylglyceryl transferase;
Reviewed.
Length = 460
Score = 29.2 bits (65), Expect = 7.2
Identities = 17/153 (11%), Positives = 39/153 (25%), Gaps = 15/153 (9%)
Query: 15 SESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSED 74
+ S+ G P + DD + +A D + + +
Sbjct: 311 AASAVGPVGPG-----EPNQP-DDVAEAVKAEVAEVTDEVAAESVVQVADRDGESTPAVE 364
Query: 75 EYVPP---KAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLSSKSGQPT 131
E + + + + +++ P A + + ++ P
Sbjct: 365 ETSEADIEREQPGDLAGQAPAAHQVDAEAASAAPEEPAALASEAHDE------TEPEVPE 418
Query: 132 KKPKLTAPSTPSTPSFPVSDTSETTPSTSGAQD 164
K + P+ P + P QD
Sbjct: 419 KAAPIPDPAKPDELAVAGPGDDPAEPDGIRRQD 451
>gnl|CDD|216648 pfam01690, PLRV_ORF5, Potato leaf roll virus readthrough protein.
This family consists mainly of the potato leaf roll
virus readthrough protein. This is generated via a
readthrough of open reading frame 3 a coat protein
allowing transcription of open reading frame 5 to give
an extended coat protein with a large c-terminal
addition or read through domain. The readthrough protein
is thought to play a role in the circulative aphid
transmission of potato leaf roll virus. Also in the
family is open reading frame 6 from beet western yellows
virus and potato leaf roll virus both luteovirus and an
unknown protein from cucurbit aphid-borne yellows virus
a closterovirus.
Length = 460
Score = 28.9 bits (65), Expect = 7.3
Identities = 29/161 (18%), Positives = 50/161 (31%), Gaps = 12/161 (7%)
Query: 42 TKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVE 101
+RP R V S + P+ Q + + PP+ E S++E+ ++E +
Sbjct: 244 VRRPPRPGHLLVVSTPELVLPPEPDEQSSERQTFKTPPQPESSSDAENGLV-SLVDEDDK 302
Query: 102 DPTPSSSEAEVTPMKNGNKRGLSSKSGQPTKKPK-----LTAPSTPSTPSFPVSDTSETT 156
+ SE++ P R L+ + P L PS T
Sbjct: 303 EEVSRDSESDAPPDDTDLTRALAEYEAAAPEVPDAARTVLQGKEQPSPDPVESPGPDLTP 362
Query: 157 PSTSGAQDWSHNHYQFLHPDHILDADRRSPKHPDYNPKTLY 197
+ + A+ R P D P T+
Sbjct: 363 GY------PKSDEVAGTYLGGGSVAEGRDPLEADPTPSTVL 397
>gnl|CDD|191602 pfam06752, E_Pc_C, Enhancer of Polycomb C-terminus. This family
represents the C-terminus of eukaryotic enhancer of
polycomb proteins, which have roles in heterochromatin
formation. This family contains several conserved
motifs.
Length = 230
Score = 28.8 bits (64), Expect = 7.4
Identities = 20/96 (20%), Positives = 33/96 (34%), Gaps = 9/96 (9%)
Query: 118 GNKRGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPS--------TSGAQDWSHNH 169
G +GL + S+ +PS + + T + + Q N+
Sbjct: 89 GVYKGLHLTRSAVPTFLPSSGGSSAGSPSGSLVRSPGHTSTNHLVPALGPASPQVLPGNN 148
Query: 170 YQFLHPDHILDADRRSPKHPDYNPKTL-YVPPEFLK 204
P H+ SP + + P+TL VP LK
Sbjct: 149 ICLSVPSHLSTVSAVSPLNVRHIPRTLAPVPSSALK 184
>gnl|CDD|165564 PHA03309, PHA03309, transcriptional regulator ICP4; Provisional.
Length = 2033
Score = 29.4 bits (65), Expect = 7.6
Identities = 32/151 (21%), Positives = 58/151 (38%), Gaps = 13/151 (8%)
Query: 12 KGDSESSTPASSKGKKTSKSPAKSEDDS--PVTKRPRRKSAKRVKSAIQSDSEPDDMLQD 69
+ S SS+ +SS S P++S S P PRR R +S + + + +
Sbjct: 1815 RSSSSSSSSSSSSSSSPSSRPSRSATPSLSPSPSPPRRAPVDRSRSGRRRERD-----RP 1869
Query: 70 NGSEDEYVPPKAEVESESEHSSGEEELEESVED------PTPSSSEAEVTPMKNGNKRGL 123
+ + + P + S + + ++ED P + S A P ++G + +
Sbjct: 1870 SANPFRWAPRQRSRADHSPDGTAPGDAPLNLEDGPGRGRPIWTPSSATTLPSRSGPEDSV 1929
Query: 124 SSKSGQPTKKPKLTAPSTPSTPSFPVSDTSE 154
+ + P APS T S+ SE
Sbjct: 1930 DETETEDSAPPARLAPSPLETSRAEDSEDSE 1960
>gnl|CDD|233367 TIGR01349, PDHac_trf_mito, pyruvate dehydrogenase complex
dihydrolipoamide acetyltransferase, long form. This
model represents one of several closely related clades
of the dihydrolipoamide acetyltransferase subunit of the
pyruvate dehydrogenase complex. It includes sequences
from mitochondria and from alpha and beta branches of
the proteobacteria, as well as from some other bacteria.
Sequences from Gram-positive bacteria are not included.
The non-enzymatic homolog protein X, which serves as an
E3 component binding protein, falls within the clade
phylogenetically but is rejected by its low score
[Energy metabolism, Pyruvate dehydrogenase].
Length = 436
Score = 29.0 bits (65), Expect = 7.8
Identities = 13/52 (25%), Positives = 17/52 (32%), Gaps = 4/52 (7%)
Query: 109 EAEVTPMKNGNKRGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTS 160
E KN S P KP AP+ P + P + +P S
Sbjct: 79 EDVADAFKNYK----LESSASPAPKPSEIAPTAPPSAPKPSPAPQKQSPEPS 126
>gnl|CDD|227091 COG4748, COG4748, Uncharacterized conserved protein [Function
unknown].
Length = 365
Score = 29.0 bits (65), Expect = 8.1
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 7/64 (10%)
Query: 39 SPVTKRPRR-----KSAKRVKSAIQSDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGE 93
+ + K + R+KSA +S+ D ++DN +DE V K ESES+ + E
Sbjct: 214 TDIVKNAFSQFINDRVNDRLKSAKKSEDTVDSGIKDNNIKDENV--KIFEESESDIITTE 271
Query: 94 EELE 97
EE+E
Sbjct: 272 EEIE 275
>gnl|CDD|215456 PLN02850, PLN02850, aspartate-tRNA ligase.
Length = 530
Score = 28.9 bits (65), Expect = 8.1
Identities = 21/86 (24%), Positives = 32/86 (37%), Gaps = 6/86 (6%)
Query: 16 ESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEPDDMLQDNGSEDE 75
S G+K SK AK K + + K+A S + DD L N +
Sbjct: 1 SSQEAVEESGEKISKKAAKKA----AAKAEKLRREATAKAAAASLEDEDDPLASNYGDVP 56
Query: 76 YVPPKAEVESE--SEHSSGEEELEES 99
+++V ++ S EEL S
Sbjct: 57 LEELQSKVTGREWTDVSDLGEELAGS 82
>gnl|CDD|222483 pfam13971, MEI4-Rec24, Microtubule-binding domain of katanin. This
is the C-terminal domain of katanin - a heterodimeric
micro-tubule severing ATPase. Katanin is found localised
at mitotic spindle bodies. This domain binds
microtubules by interacting specifically with the
N-terminal domain of p60 katanin.
Length = 375
Score = 28.7 bits (64), Expect = 8.6
Identities = 23/111 (20%), Positives = 34/111 (30%), Gaps = 17/111 (15%)
Query: 75 EYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNGNKRGLS-SKSGQPTKK 133
E + K + + E E LE +P E +KN N G + S + K
Sbjct: 44 EALAKKLKDQDEGWKKK-AELLEA---EPLQLRQEL----LKNRNSAGCAKSGAKVFPAK 95
Query: 134 ------PKLTAPSTPSTPSFPVSDTSETTPSTSGA--QDWSHNHYQFLHPD 176
T P S+ P A ++ +H QFL
Sbjct: 96 LLDQDPTSSENDETLLEELGPTPPNSQRVPKRPQADIENPFSSHMQFLQCL 146
>gnl|CDD|237632 PRK14164, PRK14164, heat shock protein GrpE; Provisional.
Length = 218
Score = 28.2 bits (63), Expect = 8.7
Identities = 19/99 (19%), Positives = 39/99 (39%), Gaps = 9/99 (9%)
Query: 4 DSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDSEP 63
S P+ GD E++ P ++ + + ++ V + A + +++
Sbjct: 3 TSNGMPDNPGDPENTDPEATSADRAEAAAEEAALAQGVPEDDPFGDAVEGEIDPDLEADL 62
Query: 64 DDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVED 102
+D+L D E+ + E S+ E +L E ED
Sbjct: 63 EDLLDD---------VDPELADDGEASTVEAQLAERTED 92
>gnl|CDD|233787 TIGR02223, ftsN, cell division protein FtsN. FtsN is a poorly
conserved protein active in cell division in a number of
Proteobacteria. The N-terminal 30 residue region tends
to by Lys/Arg-rich, and is followed by a
membrane-spanning region. This is followed by an acidic
low-complexity region of variable length and a
well-conserved C-terminal domain of two tandem regions
matched by pfam05036 (Sporulation related repeat), found
in several cell division and sporulation proteins. The
role of FtsN as a suppressor for other cell division
mutations is poorly understood; it may involve cell wall
hydrolysis [Cellular processes, Cell division].
Length = 298
Score = 28.5 bits (63), Expect = 8.8
Identities = 19/178 (10%), Positives = 46/178 (25%), Gaps = 17/178 (9%)
Query: 5 SKESPEKKGDSESSTPASSKGKKTSKSPAKSEDD--SPVTKRPRRKSAKRVKSAIQSDSE 62
SK++ E + + + + + + R + S E
Sbjct: 51 SKQANEPETLQPKNQTENGETAADLPPKPEERWSYIEELEAREVLINDPEEPSNGGGVEE 110
Query: 63 PDDMLQDNGSE------DEYVPPKAEVESESEHSSGEEELEESVEDP---------TPSS 107
+ + D K + SE + E +++ E +
Sbjct: 111 SAQLTAEQRQLLEQMQADMRAAEKVLATAPSEQTVAVEARKQTAEKKPQKARTAEAQKTP 170
Query: 108 SEAEVTPMKNGNKRGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGAQDW 165
E E K + + T + + + + P +D ++ P +
Sbjct: 171 VETEKIASKVKEAKQKQKALPKQTAETQSNSKPIETAPKADKADKTKPKPKEKAERAA 228
>gnl|CDD|217927 pfam04147, Nop14, Nop14-like family. Emg1 and Nop14 are novel
proteins whose interaction is required for the
maturation of the 18S rRNA and for 40S ribosome
production.
Length = 809
Score = 28.8 bits (65), Expect = 9.1
Identities = 14/90 (15%), Positives = 31/90 (34%), Gaps = 9/90 (10%)
Query: 54 KSAIQSDSEPDDMLQDNGSE--DEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAE 111
+ + E D + ++ + D+ + +V+ E E+E + +D E E
Sbjct: 318 QGEEDEEEEEDGVDDEDEEDDDDDLEEEEEDVDLSDEEEDEEDEDSDDEDDEEEEEEEKE 377
Query: 112 VTPMKNGNKRGLSSKSGQPTKKPKLTAPST 141
K S++S + P +
Sbjct: 378 KKKKK-------SAESTRSELPFTFPCPKS 400
>gnl|CDD|223378 COG0301, ThiI, Thiamine biosynthesis ATP pyrophosphatase [Coenzyme
metabolism].
Length = 383
Score = 28.8 bits (65), Expect = 9.4
Identities = 31/117 (26%), Positives = 46/117 (39%), Gaps = 31/117 (26%)
Query: 248 ACSYMKESGC----TGESTLLTQLCNYESQTPSGCFPDMSELLKYFENAFDHKEASSAGN 303
A +E G TGES L Q+ SQT E L+ ++ +
Sbjct: 271 AEKLAEEFGAKAIVTGES--LGQV---ASQTL--------ENLRVIDSV-------TNTP 310
Query: 304 II-PKAGVDKEYDEVMDEIKSIEKEIQTYLRTQCAHFGCTVIYSEAQKKQKKYVLEV 359
++ P G+DKE EI I + I TY + C VI++ K K ++E
Sbjct: 311 VLRPLIGLDKE------EIIEIARRIGTYEISIEPPEDCCVIFAPPTPKTKPKLIEA 361
>gnl|CDD|113839 pfam05084, GRA6, Granule antigen protein (GRA6). This family
contains the granule antigen protein GRA6 which is found
in the parasitic protozoa Toxoplasma gondii and Neospora
caninum. GRA6 protein plays an important role in the
antigenicity and pathogenicity in these organisms.
Length = 217
Score = 28.2 bits (62), Expect = 9.6
Identities = 28/122 (22%), Positives = 47/122 (38%), Gaps = 27/122 (22%)
Query: 2 YLDSKESPEKKGDSESSTPASSKGKKTSKSPAKSEDDSPVTKRPRRKSAKRVKSAIQSDS 61
S E PE G SE +S+ A++++++ +A + D
Sbjct: 56 TGSSGEPPEAVGTSEDYVNSSALAGGQDDGLAEADEEA---------------AAAEGDV 100
Query: 62 EPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEV--TPMKNGN 119
+P +L D E +E++ S EE +EE+ + P PS + TP K
Sbjct: 101 DPFPVLIDAE----------EGAAEAQGPSLEERIEEADDAPKPSPVQEAQAKTPAKRQQ 150
Query: 120 KR 121
R
Sbjct: 151 AR 152
>gnl|CDD|227952 COG5665, NOT5, CCR4-NOT transcriptional regulation complex, NOT5
subunit [Transcription].
Length = 548
Score = 28.9 bits (64), Expect = 9.8
Identities = 22/153 (14%), Positives = 42/153 (27%), Gaps = 11/153 (7%)
Query: 59 SDSEPDDMLQDNGSEDEYVPPKAEVESESEHSSGEEELEESVEDPTPSSSEAEVTPMKNG 118
++ ++ + ++ KA S + VE + S S TP
Sbjct: 214 NNQTSLSSIRSSKKQERSPKKKAPQRDVSISDRATTPIAPGVESASQSISS---TPTPVS 270
Query: 119 NKRGLSSKSGQPTKKPKLTAPSTPSTPSFPVSDTSETTPSTSGAQDWSHNHYQFLHPDHI 178
L + K ST TP+ VS + + + S Q ++ D I
Sbjct: 271 TDTPLHTVKDDSIK----FDNSTLGTPTTHVSMKKKESENDSEQQ----LNFPKDSTDEI 322
Query: 179 LDADRRSPKHPDYNPKTLYVPPEFLKKQTPCMG 211
+ + L+ +
Sbjct: 323 RKTIQHDVETNAAFQNPLFNDELKWWLASKRYL 355
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
0.311 0.128 0.375
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 28,391,621
Number of extensions: 2697572
Number of successful extensions: 3268
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3096
Number of HSP's successfully gapped: 226
Length of query: 577
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 475
Effective length of database: 6,413,494
Effective search space: 3046409650
Effective search space used: 3046409650
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 (21.8 bits)
S2: 62 (27.7 bits)