RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5289
(813 letters)
>gnl|CDD|223327 COG0249, MutS, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 843
Score = 460 bits (1185), Expect = e-150
Identities = 216/722 (29%), Positives = 338/722 (46%), Gaps = 74/722 (10%)
Query: 87 NTVGVAIVDLDTKKFYMGEIPDDDYYSNLEAIIVQKSPKECLLPAEYLNDNKNKIVTILD 146
VG+A +DL T +F++ E + L + + + PKE LL L+ +I L
Sbjct: 133 GKVGLAFIDLSTGEFFVSEFEREK----LLSELKRLQPKELLLSESLLSSTLAEIQKGLF 188
Query: 147 RNKVCMTGRKKNEFSEEDLMQDVNR---LVRFDDSELKNARLLPEMCLTTATHCLRSLIN 203
+ + F E+D + ++ + D L + L + +L++
Sbjct: 189 VVR-----LPASFFDEDDAEEILSEYFGVRDLDGFGLISTPL--ALS------AAGALLS 235
Query: 204 YLELMNNEDNMNQFSIHSIDYSK-YVHMSSAVMSSLHVLPQQGSTSAQTYDSLLGILDRC 262
YL+ + + I + Y+ + +A +L + SL +LDR
Sbjct: 236 YLKD-TQKTFLPHIQIIQRYDLEDYMVLDAATRRNLELFSNL--RGNGKKGSLFWLLDRT 292
Query: 263 RTPQGHRLLAQWMKQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMR 322
TP G RLL +W+ QPL D + I ER AV L +N E R L E L+ +PD++ L R
Sbjct: 293 VTPMGSRLLKRWLLQPLLDKEEIEERLDAVEELKDNPELREKLREM-LKKVPDLERLLSR 351
Query: 323 IGRKKAGLKDCYRVYEGVSQLP----------------KLISILESLVQNVE-------- 358
+ +A +D R+ + + ++P L+ +ESL E
Sbjct: 352 LSLGRASPRDLLRLRDSLEKIPEIFKLLSSLKSESDLLLLLEDIESLDYLAELLELLETA 411
Query: 359 -----ASNLNTILSSLQSLKMMDRKDAVMDKMKEYLESTAR--RLNLVADKTIKLENSPQ 411
+ + +D +++ KE++ R N
Sbjct: 412 INEDPPLAVRDGIIKEGYNIELDELRDLLNNAKEWIAKLELEERERTGIKSLKIKYNKVY 471
Query: 412 GFAYRITMKLNNSIDDRYTILDTVRGGVRFQDDRL-----ATANTQYQAIQREYETHQQS 466
G+ +T + D Y T++ RF L + + + + EYE
Sbjct: 472 GYYIEVTKSNAKLVPDDYIRRQTLKNAERFTTPELKELEEKLLDAEEKILALEYE----- 526
Query: 467 IVEEVIGISAGYTQTLNQLSDVLAQFDVLVSFSIASTCAPKPYVRPCMKPMGTGSLVLNQ 526
+ +E+ + L L+ LA+ DVL S A A + YVRP + + L + +
Sbjct: 527 LFDELREKILAHINELQALAKALAELDVLSSL--AEIAAEQNYVRPEF--VDSNDLEIKE 582
Query: 527 CRHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVP 586
RHP+VE ++PND+ SG L+TGPNMGGKSTY+R + + V LAQIG FVP
Sbjct: 583 GRHPVVEAVLDNGFVPNDIDL-SGNRRIILITGPNMGGKSTYLRQVALIVILAQIGSFVP 641
Query: 587 CDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGRGTST 646
+ A I +VD+IFTR+GAAD G STFM+EM ETA ++ TE SLVI+DE+GRGTST
Sbjct: 642 AEKARIGIVDRIFTRIGAADDLASGRSTFMVEMLETANILDNATERSLVILDEIGRGTST 701
Query: 647 FDGFGMACSIARELASHRQPFTLFATHFHEIALLSRVIPTFRNVQVSALEQEDNLVLLYQ 706
+DG +A ++ L TLFATH+HE+ L +P +N +SA+E+ ++ LY+
Sbjct: 702 YDGLAIAWAVLEYLHEKIGCRTLFATHYHELTELEEKLPQVKNYHMSAVEEGGDITFLYK 761
Query: 707 VKPGSCVKSYGVHCAKMAGYPEDMLEQARDLMKEYEYSLDTKTPSGDETNNREEEYFKTV 766
VKPG KSYG+H AK+AG PE+++E+AR+++ E E S E N ++ F V
Sbjct: 762 VKPGIADKSYGIHVAKLAGLPEEVIERAREILAELE---KESRSSNLELNQKDLSLFPKV 818
Query: 767 QE 768
+
Sbjct: 819 LK 820
>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 = 327 bits (842), Expect = e-107
Identities = 113/235 (48%), Positives = 159/235 (67%), Gaps = 3/235 (1%)
Query: 509 YVRPCMKPMGTGSLVLNQCRHPIVELQ-GGVSYIPNDVYFKSGEVSFNLVTGPNMGGKST 567
YVRP L + RHP+VE +++PNDV L+TGPNMGGKST
Sbjct: 1 YVRPEFTESAA--LHIEGGRHPVVEAVLDAGNFVPNDVSLGKERSRILLITGPNMGGKST 58
Query: 568 YIRSIGVSVFLAQIGCFVPCDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIK 627
Y+R + + V +AQIG FVP +SA I +VD+IFTR+GA+D G STFM+EM ETA ++
Sbjct: 59 YLRQVALIVIMAQIGSFVPAESARIGIVDRIFTRIGASDDLASGRSTFMVEMLETANILH 118
Query: 628 KCTENSLVIIDELGRGTSTFDGFGMACSIARELASHRQPFTLFATHFHEIALLSRVIPTF 687
T+ SLVI+DELGRGTST+DG +A ++A LA + TLFATH+HE+ L+ +P
Sbjct: 119 NATDKSLVILDELGRGTSTYDGLAIAWAVAEHLAEKIRARTLFATHYHELTKLAEKLPAV 178
Query: 688 RNVQVSALEQEDNLVLLYQVKPGSCVKSYGVHCAKMAGYPEDMLEQARDLMKEYE 742
+NV ++A+E ++V LY+VKPG+ KSYG+H A++AG PE ++E+AR+++ E E
Sbjct: 179 KNVHMAAVETNGDIVFLYKVKPGAADKSYGIHVAELAGLPESVVERAREVLAELE 233
>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 = 320 bits (823), Expect = e-104
Identities = 122/222 (54%), Positives = 164/222 (73%), Gaps = 2/222 (0%)
Query: 523 VLNQCRHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIG 582
VL + RHP VE Q V++IPNDV G+ F ++TGPNMGGKSTYIR IGV V +AQIG
Sbjct: 1 VLKEARHPCVEAQDDVAFIPNDVTLTRGKSRFLIITGPNMGGKSTYIRQIGVIVLMAQIG 60
Query: 583 CFVPCDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGR 642
CFVPCDSA I +VD I RVGA+DSQ +G+STFM EM ETA ++K TENSL+IIDELGR
Sbjct: 61 CFVPCDSADIPIVDCILARVGASDSQLKGVSTFMAEMLETAAILKSATENSLIIIDELGR 120
Query: 643 GTSTFDGFGMACSIARELASHRQPFTLFATHFHEIALLSRVIPTFRNVQVSAL--EQEDN 700
GTST+DGFG+A +IA +A+ + F LFATHFHE+ L+ +P +N+ V+AL +
Sbjct: 121 GTSTYDGFGLAWAIAEYIATQIKCFCLFATHFHELTALADEVPNVKNLHVTALTDDASRT 180
Query: 701 LVLLYQVKPGSCVKSYGVHCAKMAGYPEDMLEQARDLMKEYE 742
L +LY+V+ G+C +S+G+H A++A +P++++E A+ E E
Sbjct: 181 LTMLYKVEKGACDQSFGIHVAELANFPKEVIEMAKQKALELE 222
>gnl|CDD|233259 TIGR01070, mutS1, DNA mismatch repair protein MutS. [DNA
metabolism, DNA replication, recombination, and repair].
Length = 840
Score = 339 bits (872), Expect = e-104
Identities = 209/753 (27%), Positives = 327/753 (43%), Gaps = 111/753 (14%)
Query: 76 SEDKTLETVLT--NTVGVAIVDLDTKKFYMGEIPDDDYYSNLEAIIVQKSPKECLLPAEY 133
+D L + N G+A +DL T +F + E+ D L A + + +P E LL +
Sbjct: 119 RQDNLLAAIAQESNGFGLATLDLTTGEFKVTELAD---KETLYAELQRLNPAEVLLAEDL 175
Query: 134 LNDNKNKIVTILDRNKVCMTGRKKNEFSEEDLMQDVNRL-VRFDDSELKNARLLPEMCLT 192
I R T E +D+ L +R L A L L
Sbjct: 176 SEME-----AIELREFRKDTAVMSLEAQFGT--EDLGGLGLRNAPLGLTAAGCL----LQ 224
Query: 193 TATHCLRSLINYLELMNNEDNMNQFSIHSIDYSKYVHMSSAVMSSLHVLPQQGSTSAQTY 252
A R+ + +L+ + + ++ + +A +L + +
Sbjct: 225 YAKRTQRTALPHLQ-----------PVRLYELQDFMQLDAATRRNLELTE---NLRGGKQ 270
Query: 253 DSLLGILDRCRTPQGHRLLAQWMKQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRG 312
++L +LD +T G RLL +W+ +PL+D + + R V +L+ + R L L+
Sbjct: 271 NTLFSVLDETKTAMGSRLLKRWLHRPLRDREVLEARQDTVEVLLRHFFLREGLRPL-LKE 329
Query: 313 LPDMQSLAMRIGRKKAGLKDCYRVYEGVSQLPKLISILESLVQNVEASNLNTI--LSSLQ 370
+ D++ LA R+ A +D R+ + QLP+L ++LE L + I S L
Sbjct: 330 VGDLERLAARVALGNARPRDLARLRTSLEQLPELRALLEELEGPTLQALAAQIDDFSELL 389
Query: 371 SL------------------------KMMDRKDAVMDKMKEYLES-TARRLNLVADKTIK 405
L + +D A + +YL AR T+K
Sbjct: 390 ELLEAALIENPPLVVRDGGLIREGYDEELDELRAASREGTDYLARLEARERERTGIPTLK 449
Query: 406 -----------------LENSPQGFAYRITMKLNNSIDDRYTILDTVRGGVRFQDDRLAT 448
L P + R T+K N+ +RY + +D L
Sbjct: 450 VGYNAVFGYYIEVTRGQLHLVPAHYRRRQTLK--NA--ERYITPELKE----KEDKVLEA 501
Query: 449 ANTQYQAIQREYETHQQSIVEEVIGISAGYTQTLNQLSDVLAQFDVLVSFSIASTCAPKP 508
+ + E E + EE+ + Y + L + + LA+ DVL + A
Sbjct: 502 EG---KILALEKE-----LFEELRELLKKYLEALQEAARALAELDVLANL--AEVAETLH 551
Query: 509 YVRP--CMKPMGTGSLVLNQCRHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKS 566
Y RP P L + + RHP+VE ++PND+ + L+TGPNMGGKS
Sbjct: 552 YTRPRFGDDP----QLRIREGRHPVVEQVLRTPFVPNDLEM-AHNRRMLLITGPNMGGKS 606
Query: 567 TYIRSIGVSVFLAQIGCFVPCDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVI 626
TY+R + LAQIG FVP +SA + + D+IFTR+GA+D G STFM+EM E A ++
Sbjct: 607 TYMRQTALIALLAQIGSFVPAESAELPLFDRIFTRIGASDDLASGRSTFMVEMTEAANIL 666
Query: 627 KKCTENSLVIIDELGRGTSTFDGFGMACSIARELASHRQPFTLFATHFHEIALLSRVIPT 686
TENSLV+ DE+GRGTST+DG +A +IA L H + TLFATH+ E+ L +P
Sbjct: 667 HNATENSLVLFDEIGRGTSTYDGLALAWAIAEYLHEHIRAKTLFATHYFELTALEESLPG 726
Query: 687 FRNVQVSALEQEDNLVLLYQVKPGSCVKSYGVHCAKMAGYPEDMLEQARDLMKEYEYSLD 746
+NV V+ALE +V L+QV PG KSYG+ A +AG P++++ +AR ++ + E
Sbjct: 727 LKNVHVAALEHNGTIVFLHQVLPGPASKSYGLAVAALAGLPKEVIARARQILTQLEAR-- 784
Query: 747 TKTPSGDETNNREEEYFKTVQEGEYQMFDFLQQ 779
+ E K Q+ F +
Sbjct: 785 --------STESEAPQRKAQTSAPEQISLFDEA 809
>gnl|CDD|235444 PRK05399, PRK05399, DNA mismatch repair protein MutS; Provisional.
Length = 854
Score = 334 bits (860), Expect = e-102
Identities = 128/315 (40%), Positives = 193/315 (61%), Gaps = 15/315 (4%)
Query: 444 DRLATANTQYQAIQREYETHQQSIVEEVIGISAGYTQTLNQLSDVLAQFDVLVSFS-IAS 502
D++ +A + A+ EYE ++ + EEV A + + L +L+ LA+ DVL S + +A
Sbjct: 510 DKILSAEEK--ALALEYELFEE-LREEV----AEHIERLQKLAKALAELDVLASLAEVAE 562
Query: 503 TCAPKPYVRPCMKPMGTGSLVLNQCRHPIVE-LQGGVSYIPNDVYFKSGEVSFNLVTGPN 561
YVRP + + + RHP+VE + GG ++PND E L+TGPN
Sbjct: 563 ENN---YVRPEFTD--DPGIDIEEGRHPVVEQVLGGEPFVPNDCDL-DEERRLLLITGPN 616
Query: 562 MGGKSTYIRSIGVSVFLAQIGCFVPCDSATISVVDQIFTRVGAADSQYRGISTFMMEMKE 621
M GKSTY+R + + V LAQIG FVP +SA I +VD+IFTR+GA+D G STFM+EM E
Sbjct: 617 MAGKSTYMRQVALIVLLAQIGSFVPAESARIGIVDRIFTRIGASDDLASGRSTFMVEMTE 676
Query: 622 TATVIKKCTENSLVIIDELGRGTSTFDGFGMACSIARELASHRQPFTLFATHFHEIALLS 681
TA ++ TE SLV++DE+GRGTST+DG +A ++A L TLFATH+HE+ L
Sbjct: 677 TANILNNATERSLVLLDEIGRGTSTYDGLSIAWAVAEYLHDKIGAKTLFATHYHELTELE 736
Query: 682 RVIPTFRNVQVSALEQEDNLVLLYQVKPGSCVKSYGVHCAKMAGYPEDMLEQARDLMKEY 741
+P +NV V+ E ++V L++V PG+ KSYG+H AK+AG P ++++AR+++ +
Sbjct: 737 EKLPGVKNVHVAVKEHGGDIVFLHKVVPGAADKSYGIHVAKLAGLPASVIKRAREILAQL 796
Query: 742 EYSLDTKTPSGDETN 756
E + + + E +
Sbjct: 797 ESASEKAKAASAEED 811
Score = 118 bits (299), Expect = 3e-27
Identities = 71/304 (23%), Positives = 132/304 (43%), Gaps = 36/304 (11%)
Query: 72 LCVISEDKTLETVLTNTVGVAIVDLDTKKFYMGEIPDDDYYSNLEAIIVQKSPKECLLPA 131
L I++D G+A +DL T +F + E+ +++ + L + +P E L+P
Sbjct: 131 LAAIAQDG-------GGYGLAYLDLSTGEFRVTELDEEELLAELARL----NPAEILVPE 179
Query: 132 EYLNDNKNKIVTILDRNKVCMTGRKKNEFSEEDLMQDVNRLVRFDDSELKNARLLPEMCL 191
++ D L + + R EF + + + F + L + L
Sbjct: 180 DFSEDE-------LLLLRRGLRRRPPWEFDLDTAEKRLLEQ--FGVASLDGFGVD----L 226
Query: 192 TTATHCLRSLINYLE--LMNNEDNMNQFSIHSIDYSKYVHMSSAVMSSLHVLPQQGSTSA 249
A +L+ YL+ + ++ + S Y+ + +A +L + +
Sbjct: 227 PLAIRAAGALLQYLKETQKRSLPHLRSPKRYEE--SDYLILDAATRRNLELTE---NLRG 281
Query: 250 QTYDSLLGILDRCRTPQGHRLLAQWMKQPLKDLDAIVERHAAVNILVNNTEARMNLHEYA 309
+SLL +LDR T G RLL +W+ +PL+D +AI R AV L+ + R +L E
Sbjct: 282 GRKNSLLSVLDRTVTAMGGRLLRRWLHRPLRDREAIEARLDAVEELLEDPLLREDLREL- 340
Query: 310 LRGLPDMQSLAMRIGRKKAGLKDCYRVYEGVSQLPKLISILESLVQNVEASNLNTILSSL 369
L+G+ D++ L RI +A +D + + + LP+L +L L ++ L + L
Sbjct: 341 LKGVYDLERLLSRIALGRANPRDLAALRDSLEALPELKELLAEL----DSPLLAELAEQL 396
Query: 370 QSLK 373
L+
Sbjct: 397 DPLE 400
>gnl|CDD|197777 smart00534, MUTSac, ATPase domain of DNA mismatch repair MUTS
family.
Length = 185
Score = 277 bits (712), Expect = 8e-89
Identities = 96/185 (51%), Positives = 138/185 (74%)
Query: 554 FNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVPCDSATISVVDQIFTRVGAADSQYRGIS 613
++TGPNMGGKSTY+R + + V +AQIG FVP +SA + V D+IFTR+GA+DS +G+S
Sbjct: 1 VVIITGPNMGGKSTYLRQVALIVIMAQIGSFVPAESAELPVFDRIFTRIGASDSLAQGLS 60
Query: 614 TFMMEMKETATVIKKCTENSLVIIDELGRGTSTFDGFGMACSIARELASHRQPFTLFATH 673
TFM+EMKETA ++K T+NSLV++DELGRGTST+DG +A +I L TLFATH
Sbjct: 61 TFMVEMKETANILKNATKNSLVLLDELGRGTSTYDGLAIAAAILEYLLEKIGARTLFATH 120
Query: 674 FHEIALLSRVIPTFRNVQVSALEQEDNLVLLYQVKPGSCVKSYGVHCAKMAGYPEDMLEQ 733
+HE+ L+ P RN+ +SALE+ +N+ LY++KPG KSYG+ AK+AG P++++E+
Sbjct: 121 YHELTKLADNHPGVRNLHMSALEETENITFLYKLKPGVAGKSYGIEVAKLAGLPKEVIER 180
Query: 734 ARDLM 738
A+ ++
Sbjct: 181 AKRIL 185
>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 = 275 bits (706), Expect = 2e-87
Identities = 97/212 (45%), Positives = 138/212 (65%), Gaps = 2/212 (0%)
Query: 528 RHPIVE-LQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVP 586
RHP+VE + ++PND E L+TGPNM GKSTY+R + + LAQIG FVP
Sbjct: 6 RHPVVEQVLDNEPFVPNDTEL-DPERQILLITGPNMAGKSTYLRQVALIALLAQIGSFVP 64
Query: 587 CDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGRGTST 646
A I VVD+IFTR+GA+D G STFM+EM ETA ++ TE SLV++DE+GRGTST
Sbjct: 65 ASKAEIGVVDRIFTRIGASDDLAGGRSTFMVEMVETANILNNATERSLVLLDEIGRGTST 124
Query: 647 FDGFGMACSIARELASHRQPFTLFATHFHEIALLSRVIPTFRNVQVSALEQEDNLVLLYQ 706
+DG +A +I L TLFATH+HE+ L +P +N V+ E+ +V L++
Sbjct: 125 YDGLSIAWAIVEYLHEKIGAKTLFATHYHELTELEGKLPRVKNFHVAVKEKGGGVVFLHK 184
Query: 707 VKPGSCVKSYGVHCAKMAGYPEDMLEQARDLM 738
+ G+ KSYG+ A++AG PE+++E+AR+++
Sbjct: 185 IVEGAADKSYGIEVARLAGLPEEVIERAREIL 216
>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 = 239 bits (611), Expect = 6e-74
Identities = 96/204 (47%), Positives = 131/204 (64%), Gaps = 4/204 (1%)
Query: 523 VLNQCRHPIVE-LQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQI 581
+ RHP++ L G +++PND+ SG L+TGPNMGGKSTY+RSIG++V LAQI
Sbjct: 1 EIKGGRHPVLLALTKGETFVPNDINLGSG--RLLLITGPNMGGKSTYLRSIGLAVLLAQI 58
Query: 582 GCFVPCDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELG 641
GCFVP +SA+I +VD+IFTR+GA DS G STFM E+ E ++ T SLV+IDELG
Sbjct: 59 GCFVPAESASIPLVDRIFTRIGAEDSISDGRSTFMAELLELKEILSLATPRSLVLIDELG 118
Query: 642 RGTSTFDGFGMACSIARELASHRQPFTLFATHFHEIALLSRVIPTFRNVQVSALEQEDNL 701
RGTST +G +A ++ L + TLFATHFHE+A L +P +N+ + L L
Sbjct: 119 RGTSTAEGLAIAYAVLEHLLE-KGCRTLFATHFHELADLPEQVPGVKNLHMEELITTGGL 177
Query: 702 VLLYQVKPGSCVKSYGVHCAKMAG 725
Y++ G C SY + A++AG
Sbjct: 178 TFTYKLIDGICDPSYALQIAELAG 201
>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 = 226 bits (579), Expect = 4e-69
Identities = 85/216 (39%), Positives = 134/216 (62%), Gaps = 9/216 (4%)
Query: 528 RHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVPC 587
RHP++E S++PND++ + ++TGPNMGGKS+YIR + + +AQIG FVP
Sbjct: 7 RHPMIESLLDKSFVPNDIHLSAEGGYCQIITGPNMGGKSSYIRQVALITIMAQIGSFVPA 66
Query: 588 DSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGRGTSTF 647
SAT+S+ D + TR+GA+DS G+STFM+E+ ET+ ++ CT SLVI+DELGRGTST
Sbjct: 67 SSATLSIFDSVLTRMGASDSIQHGMSTFMVELSETSHILSNCTSRSLVILDELGRGTSTH 126
Query: 648 DGFGMACSIARELASHRQPFTLFATHFHEIALLSRVIP-TFRNVQVSALEQE-------- 698
DG +A + L ++ LF TH+ + + R + RN +S LE +
Sbjct: 127 DGIAIAYATLHYLLEEKKCLVLFVTHYPSLGEILRRFEGSIRNYHMSYLESQKDFETSDS 186
Query: 699 DNLVLLYQVKPGSCVKSYGVHCAKMAGYPEDMLEQA 734
++ LY++ G +S+G++ A++AG P+ ++ +A
Sbjct: 187 QSITFLYKLVRGLASRSFGLNVARLAGLPKSIISRA 222
>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 = 218 bits (557), Expect = 6e-66
Identities = 87/217 (40%), Positives = 135/217 (62%), Gaps = 6/217 (2%)
Query: 524 LNQCRHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGC 583
+ RHP + S++PNDV + ++TGPNMGGKST +R++ ++V +AQ+G
Sbjct: 2 FEELRHPCLNASTASSFVPNDVDLGATSPRILVLTGPNMGGKSTLLRTVCLAVIMAQMGM 61
Query: 584 FVPCDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGRG 643
VP S +S+VD+IFTR+GA D +G STFM+E+ ETA +++ T +SLVI+DELGRG
Sbjct: 62 DVPAKSMRLSLVDRIFTRIGARDDIMKGESTFMVELSETANILRHATPDSLVILDELGRG 121
Query: 644 TSTFDGFGMACSIARELASHRQPFTLFATHFHEIALLSRVIPTFRNVQVS-ALEQEDN-- 700
TST DG+ +A ++ L + TLF+TH+H + R ++ A++ E +
Sbjct: 122 TSTHDGYAIAHAVLEYLVKKVKCLTLFSTHYHSLCDEFHEHGGVRLGHMACAVKNESDPT 181
Query: 701 ---LVLLYQVKPGSCVKSYGVHCAKMAGYPEDMLEQA 734
+ LY++ G C KSYG++ A MAG P+ ++E+A
Sbjct: 182 IRDITFLYKLVAGICPKSYGLYVALMAGIPDGVVERA 218
>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 = 199 bits (507), Expect = 6e-59
Identities = 80/208 (38%), Positives = 122/208 (58%), Gaps = 11/208 (5%)
Query: 528 RHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVPC 587
RHP++EL S++PND G S ++TGPN GKS Y++ + + VFLA IG FVP
Sbjct: 6 RHPLLELFVD-SFVPNDTEIGGGGPSIMVITGPNSSGKSVYLKQVALIVFLAHIGSFVPA 64
Query: 588 DSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGRGTSTF 647
DSATI +VD+IFTR+ + +S G S FM+++ + + ++ T SLV+IDE G+GT T
Sbjct: 65 DSATIGLVDKIFTRMSSRESVSSGQSAFMIDLYQVSKALRLATRRSLVLIDEFGKGTDTE 124
Query: 648 DGFGMACSIARELASH--RQPFTLFATHFHEI----ALLSRVIPTFRNVQV----SALEQ 697
DG G+ + L P + +THFHE+ L R+ F ++V ++
Sbjct: 125 DGAGLLIATIEHLLKRGPECPRVIVSTHFHELFNRSLLPERLKIKFLTMEVLLNPTSTSP 184
Query: 698 EDNLVLLYQVKPGSCVKSYGVHCAKMAG 725
+++ LY++ PG S+ +HCAK+AG
Sbjct: 185 NEDITYLYRLVPGLADTSFAIHCAKLAG 212
>gnl|CDD|214710 smart00533, MUTSd, DNA-binding domain of DNA mismatch repair MUTS
family.
Length = 308
Score = 174 bits (443), Expect = 8e-49
Identities = 83/314 (26%), Positives = 142/314 (45%), Gaps = 40/314 (12%)
Query: 254 SLLGILDRCRTPQGHRLLAQWMKQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGL 313
SL +L+ +TP G RLL +W+ QPL DL I ER AV LV N E R L + L+ +
Sbjct: 3 SLFELLNHTKTPMGKRLLRRWLLQPLLDLKEINERLDAVEELVENPELRQKLRQL-LKRI 61
Query: 314 PDMQSLAMRIGRKKAGLKDCYRVYEGVSQLPKLISILESLVQNVEASNLNTILSSLQSL- 372
PD++ L RI R +A +D R+Y+ + L ++ +LESL + L IL L L
Sbjct: 62 PDLERLLSRIERGRASPRDLLRLYDSLEGLKEIRQLLESLDGPLLGLLLKVILEPLLELL 121
Query: 373 ------------------------------KMMDRKDAVMDKMKEYLESTARRLNLVADK 402
++ ++ + + ++++E L+ L +
Sbjct: 122 ELLLELLNDDDPLEVNDGGLIKDGFDPELDELREKLEELEEELEELLKKEREELGI---D 178
Query: 403 TIKLENSPQ-GFAYRITMKLNNSIDDRYTILDTVRGGVRFQDDRLATANTQYQAIQREYE 461
++KL + G+ +T + + +++ RF L + + E E
Sbjct: 179 SLKLGYNKVHGYYIEVTKSEAKKVPKDFIRRSSLKNTERFTTPELKELENELLEAKEEIE 238
Query: 462 THQQSIVEEVIGISAGYTQTLNQLSDVLAQFDVLVSFSIASTCAPKPYVRPCMKPMGTGS 521
++ I+ E++ Y + L L++ LA+ DVL+S + + A YVRP +G
Sbjct: 239 RLEKEILRELLEKVLEYLEELRALAEALAELDVLLSLATLA--AEGNYVRPEFVD--SGE 294
Query: 522 LVLNQCRHPIVELQ 535
L + RHP++ELQ
Sbjct: 295 LEIKNGRHPVLELQ 308
>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 = 166 bits (422), Expect = 3e-47
Identities = 73/199 (36%), Positives = 115/199 (57%), Gaps = 4/199 (2%)
Query: 526 QCRHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFV 585
RHPI++ +IPND+Y G F+++TGPNM GKSTY++ I + +AQIGCFV
Sbjct: 4 DSRHPILDRDKKN-FIPNDIYLTRGSSRFHIITGPNMSGKSTYLKQIALLAIMAQIGCFV 62
Query: 586 PCDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGRGTS 645
P + AT+ + +++ +R+ DS R +STF EM ETA ++ +SLV+IDELGRGTS
Sbjct: 63 PAEYATLPIFNRLLSRLSNDDSMERNLSTFASEMSETAYILDYADGDSLVLIDELGRGTS 122
Query: 646 TFDGFGMACSIARELASHRQPFTLFATHFHEIALLSRVIPTFRNVQVSALEQEDN-LVLL 704
+ DGF ++ +I L ++ FATHF +IA + ++ + A N + +
Sbjct: 123 SADGFAISLAILECL-IKKESTVFFATHFRDIAAILGNKSCVVHLHMKAQSINSNGIEMA 181
Query: 705 YQVKPGS-CVKSYGVHCAK 722
Y++ G + G+ +
Sbjct: 182 YKLVLGLYRIVDDGIRFVR 200
>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 = 134 bits (338), Expect = 8e-35
Identities = 71/302 (23%), Positives = 129/302 (42%), Gaps = 45/302 (14%)
Query: 232 SAVMSSLHVLPQQGSTSAQTYDSLLGILDRCRTPQGHRLLAQWMKQPLKDLDAIVERHAA 291
+A + +L + + SLLG+LDR TP G RLL +W+ +PL DLD I R A
Sbjct: 1 AATLRNLELFR---NLRGGKKGSLLGLLDRTVTPMGKRLLRRWLLRPLTDLDEINARLDA 57
Query: 292 VNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCYRVYEGVSQLPKLISILE 351
V L+ + R L E AL+G+PD++ L R+ +A +D + + LP L +L
Sbjct: 58 VEELLEDL--REELRE-ALKGIPDLERLLSRLALGRASPRDLLALRSSLEALPALRKLLA 114
Query: 352 SLVQNVEASNLNTILSSLQSLKMMDR----------------------KDAVMDKMKEYL 389
S A L + L ++++ D +D+++ L
Sbjct: 115 S------APLLADLADQLPLPELLELLERAIDEDPPLSLRDGGVIKDGYDPELDELRALL 168
Query: 390 ESTARRLNLVADK--------TIKLENSPQGFAYRI--TMKLNNSIDDRYTILDTVRGGV 439
+ +L + ++ ++K+ + Y I + + Y T + V
Sbjct: 169 DELREKLAELLERERERTGIKSLKVGYNRVFGYYVIEVKASKADKVPGDYIRRSTTKNAV 228
Query: 440 RFQDDRLATANTQYQAIQREYETHQQSIVEEVIG-ISAGYTQTLNQLSDVLAQFDVLVSF 498
RF L + + ++ I+EE++ + + Y + L +L+D +A+ DVL+S
Sbjct: 229 RFTTPELKELERKLLEAEERALALEKEILEELLERVLSEYAELLQELADAIAELDVLLSL 288
Query: 499 SI 500
+
Sbjct: 289 AE 290
>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 = 128 bits (325), Expect = 4e-34
Identities = 57/201 (28%), Positives = 100/201 (49%), Gaps = 9/201 (4%)
Query: 528 RHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVPC 587
HP++ + V+ ND+ + + L+TG NM GKST++R+IGV+V LAQ G V
Sbjct: 6 GHPLIGREKRVA---NDIDM--EKKNGILITGSNMSGKSTFLRTIGVNVILAQAGAPVCA 60
Query: 588 DSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIK--KCTENSLVIIDELGRGTS 645
S + V IFT + +D GIS F E++ +++ K E L ++DE+ +GT+
Sbjct: 61 SSFELPPVK-IFTSIRVSDDLRDGISYFYAELRRLKEIVEKAKKGEPVLFLLDEIFKGTN 119
Query: 646 TFDGFGMACSIARELASHRQPFTLFATHFHEIALLSRVIPTFRNVQVSALEQEDNLVLLY 705
+ + + ++ + L + + + +TH E+A L + RN ++ L+ Y
Sbjct: 120 SRERQAASAAVLKFLKN-KNTIGIISTHDLELADLLDLDSAVRNYHFREDIDDNKLIFDY 178
Query: 706 QVKPGSCVKSYGVHCAKMAGY 726
++KPG + K G
Sbjct: 179 KLKPGVSPTRNALRLMKKIGI 199
>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 = 113 bits (285), Expect = 1e-28
Identities = 51/167 (30%), Positives = 87/167 (52%), Gaps = 4/167 (2%)
Query: 524 LNQCRHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGC 583
L + RHP++ LQG +P D+ + ++TGPN GGK+ ++++G+ +AQ G
Sbjct: 2 LREARHPLLPLQGEKV-VPLDIQLGENKRVL-VITGPNAGGKTVTLKTLGLLTLMAQSGL 59
Query: 584 FVPCD-SATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGR 642
+P +++ V + IF +G S + +STF MK A +++ +SLV++DELG
Sbjct: 60 PIPAAEGSSLPVFENIFADIGDEQSIEQSLSTFSSHMKNIARILQHADPDSLVLLDELGS 119
Query: 643 GTSTFDGFGMACSIARELASHRQPFTLFATHFHEIALLSRVIPTFRN 689
GT +G +A +I EL R + TH+ E+ + N
Sbjct: 120 GTDPVEGAALAIAILEELLE-RGALVIATTHYGELKAYAYKREGVEN 165
>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 = 122 bits (308), Expect = 1e-28
Identities = 115/502 (22%), Positives = 210/502 (41%), Gaps = 53/502 (10%)
Query: 328 AGLKDCYRVYEGVSQLPKLISILESLVQNVEASNL-NTILSSL-QSLKMMDRKDAVMDKM 385
+K + E V L L + + L N I++ + K+ D +D +
Sbjct: 95 KTVKHLKVLSEHVLDLEILFHLRL---NLITLPPLENDIIACIDDDGKVKDGASEELDAI 151
Query: 386 KEYLESTARRLNLVADKTIKLENSPQGFAYRITMKLNNSIDDRYTILDTVRGGVRFQ--- 442
+E L++ + K I+ + + + I N RY + ++ G + +
Sbjct: 152 RESLKALEEEVVKRLHKIIRSKELAKYLSDTIVTIRN----GRYVLP--LKSGFKGKIKG 205
Query: 443 --DDRLATANTQY---QAIQ------REYETHQQSIVEEVI-GISAGYTQTLNQLSDVLA 490
D ++ T Y QAI + + ++ +E+++ +S + L +L +
Sbjct: 206 IVHDTSSSGETFYIEPQAIVKLNNKLAQLKNEEECEIEKILRTLSEKVQEYLLELKFLFK 265
Query: 491 QFDVL------VSFSIASTCAPKPYVRPCMKPMGTGSLVLNQCRHPIVELQGGVSYIPND 544
+FD L ++ A P P TG ++L RHP+++ +P
Sbjct: 266 EFDFLDSLQARARYAKA-VKGEFP------MPSFTGKIILENARHPLLKEP---KVVPFT 315
Query: 545 VYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVPCD-SATISVVDQIFTRVG 603
+ K E +TGPN GGK+ ++++G+ + Q G +P + + I ++IF +G
Sbjct: 316 LNLKF-EKRVLAITGPNTGGKTVTLKTLGLLALMFQSGIPIPANEHSEIPYFEEIFADIG 374
Query: 604 AADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGRGTSTFDGFGMACSIARELASH 663
S + +STF MK + ++ K TENSLV+ DELG GT +G +A SI L
Sbjct: 375 DEQSIEQNLSTFSGHMKNISAILSKTTENSLVLFDELGAGTDPDEGSALAISILEYL--L 432
Query: 664 RQP-FTLFATHFHEIALLSRVIPTFRNVQVSALEQEDNLVLLYQVKPGSCVKSYGVHCAK 722
+Q L TH+ E+ L N S L E+ L Y++ G +SY A+
Sbjct: 433 KQNAQVLITTHYKELKALMYNNEGVEN--ASVLFDEETLSPTYKLLKGIPGESYAFEIAQ 490
Query: 723 MAGYPEDMLEQARDLMKEYEYSLDTKTPSGDETNNREEEYF----KTVQEGEYQMFDFLQ 778
G P ++EQA+ E++ ++ E+ K ++E E + Q
Sbjct: 491 RYGIPHFIIEQAKTFYGEFKEEINVLIEKLSALEKELEQKNEHLEKLLKEQEKLKKELEQ 550
Query: 779 QCLSLSKQKDTNRILHLQETQE 800
+ L +++ ++ +E QE
Sbjct: 551 EMEELKERERNKKLELEKEAQE 572
>gnl|CDD|213194 cd03227, ABC_Class2, ATP-binding cassette domain of non-transporter
proteins. ABC-type Class 2 contains systems involved in
cellular processes other than transport. These families
are characterized by the fact that the ABC subunit is
made up of duplicated, fused ABC modules (ABC2). No
known transmembrane proteins or domains are associated
with these proteins.
Length = 162
Score = 107 bits (268), Expect = 7e-27
Identities = 50/166 (30%), Positives = 76/166 (45%), Gaps = 29/166 (17%)
Query: 531 IVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLA----------Q 580
IV + ++PNDV F GE S ++TGPN GKST + +IG+++ A +
Sbjct: 2 IVLGRFPSYFVPNDVTF--GEGSLTIITGPNGSGKSTILDAIGLALGGAQSATRRRSGVK 59
Query: 581 IGCFVPCDSATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTEN--SLVIID 638
GC V SA + IFTR+ +S E+ A ++ + L I+D
Sbjct: 60 AGCIVAAVSAEL-----IFTRL--------QLSGGEKELSALALILALASLKPRPLYILD 106
Query: 639 ELGRGTSTFDGFGMACSIARELASHRQPFTLFATHFHEIALLSRVI 684
E+ RG DG +A +I L Q + TH E+A L+ +
Sbjct: 107 EIDRGLDPRDGQALAEAILEHLVKGAQ--VIVITHLPELAELADKL 150
>gnl|CDD|234750 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 107 bits (271), Expect = 4e-24
Identities = 86/348 (24%), Positives = 151/348 (43%), Gaps = 58/348 (16%)
Query: 425 IDDRYTILDTVRGGVRFQD-------DRLATANTQY---QAI--------------QREY 460
+DRY + V+ ++ D+ ++ T Y Q++ ++E
Sbjct: 192 RNDRYVLP--VKAE--YKHAIKGIVHDQSSSGATLYIEPQSVVELNNEIRELRNKEEQEI 247
Query: 461 ETHQQSIVEEVIGISAGYTQTLNQLSDVLAQFDVL---VSFSIASTCAPKPYVRPCMKPM 517
E + + +V A L L+ + + D + ++ A P
Sbjct: 248 ERILKELSAKV----AKNLDFLKFLNKIFDELDFIFARARYAKA-----LKATFP--LFN 296
Query: 518 GTGSLVLNQCRHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVF 577
G + L Q RHP+++ + V P D+ + + ++TGPN GGK+ ++++G++
Sbjct: 297 DEGKIDLRQARHPLLDGEKVV---PKDISL-GFDKTVLVITGPNTGGKTVTLKTLGLAAL 352
Query: 578 LAQIGCFVPCDS-ATISVVDQIFTRVGAADSQYRGISTFMMEMKETATVIKKCTENSLVI 636
+A+ G +P + + I V +IF +G S + +STF M +++K +NSLV+
Sbjct: 353 MAKSGLPIPANEPSEIPVFKEIFADIGDEQSIEQSLSTFSGHMTNIVRILEKADKNSLVL 412
Query: 637 IDELGRGTSTFDGFGMACSIARELASHRQPFTLFATHFHEIALLSRVIPTFRNVQVSALE 696
DELG GT +G +A SI L + TH+ E+ L N S
Sbjct: 413 FDELGAGTDPDEGAALAISILEYLRKRGA-KIIATTHYKELKALMYNREGVEN--ASVEF 469
Query: 697 QEDNLV----LLYQVKPGSCVKSYGVHCAKMAGYPEDMLEQARDLMKE 740
E+ L LL + PG KS AK G PE+++E+A+ L+ E
Sbjct: 470 DEETLRPTYRLLIGI-PG---KSNAFEIAKRLGLPENIIEEAKKLIGE 513
>gnl|CDD|224114 COG1193, COG1193, Mismatch repair ATPase (MutS family) [DNA
replication, recombination, and repair].
Length = 753
Score = 106 bits (267), Expect = 1e-23
Identities = 116/564 (20%), Positives = 217/564 (38%), Gaps = 61/564 (10%)
Query: 276 KQPLKDLDAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAG------ 329
+ LK+L + L EA L + L L + ++ +GR + G
Sbjct: 26 LEELKNLKPRTDLELIEEELSETAEALDILEDEGLPPLGGLNDVSEALGRLEKGGRLHVE 85
Query: 330 -LKDCYRVYEGVSQLPKLISILE-----SLVQNVEASNL--NTILSSLQSLKMMDRKDAV 381
L + G L + I LE + +E S+L + + DR
Sbjct: 86 ELLEISDFLRGFRALKRAIKKLERIKRTLALALIELSDLELEINIPIDDDGLIKDRASFE 145
Query: 382 MDKMKEYLESTARRLNLVADKTIKLENSPQGFAYRITMKLNNSIDDRYTIL------DTV 435
+D ++ L + + I+ + + + ++ + D R + +
Sbjct: 146 LDAIRRQLRDLEEEIRDKLESLIRSKEAK-----YLQDRIVTTRDGREVLPVKAEFKGAI 200
Query: 436 RGGVRFQDDRLATANT---QYQAIQREYETHQQSIVEEVIGISAGYTQTLNQLSDVLAQF 492
+G V D ++ T + +++ + + +VEE + ++ V+ +
Sbjct: 201 KGIVH---DTSSSGATLYIEPRSVVKLNNELRALLVEEDEEEERILRELSALVAPVIPEL 257
Query: 493 DVLVSF--------SIASTCAPKPYVRPCMKPMGTGSLVLNQCRHPIVELQGGVSYIPND 544
++L+ + V+P G L L RHP+++ +PND
Sbjct: 258 EILLEIIGELDFIEAKVRYAKALKGVKPDFSN--DGVLELLDARHPLLKED-----VPND 310
Query: 545 VYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVPCDSAT-ISVVDQIFTRVG 603
+ E+ ++TGPN GGK+ ++++G+ +AQ G +P + + V +IF +G
Sbjct: 311 LELGE-ELDRLIITGPNTGGKTVTLKTLGLLRLMAQSGLPIPALEGSELPVFVKIFADIG 369
Query: 604 AADSQYRGISTFMMEMKETATVIKKCTENSLVIIDELGRGTSTFDGFGMACSIARELASH 663
S + +STF M +++K +SLV+ DELG GT +G +A +I +L
Sbjct: 370 DEQSIEQSLSTFSSHMTNIVEILEK--ADSLVLFDELGSGTDPDEGAALAIAILEDL--L 425
Query: 664 RQPFTLFA-THFHEIALLSRVIPTFRNVQVSALEQEDNLVLLYQVKPGSCVKSYGVHCAK 722
+P + A TH+ E+ L+ N S + L Y++ G +S A
Sbjct: 426 EKPAKIVATTHYRELKALAAEREGVEN--ASMEFDAETLRPTYRLLEGVPGRSNAFDIAL 483
Query: 723 MAGYPEDMLEQARDLMKEYEYSLDTKTPSGDETNNR--EEEYF---KTVQEGEYQMFDFL 777
G PE ++E+A+ E + L+ + E + EEE K + E E
Sbjct: 484 RLGLPEPIIEEAKTEFGEEKELLE-ELIEKLEEVRKELEEELEEVEKLLDEVELLTGANS 542
Query: 778 QQCLSLSKQKDTNRILHLQETQEP 801
SL + K +L P
Sbjct: 543 GGKTSLLELKAQIVVLAHMGLPVP 566
>gnl|CDD|218486 pfam05188, MutS_II, MutS domain II. This domain is found in
proteins of the MutS family (DNA mismatch repair
proteins) and is found associated with pfam00488,
pfam01624, 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. This domain corresponds to
domain II in Thermus aquaticus MutS as characterized in,
and has similarity resembles RNAse-H-like domains (see
pfam00075).
Length = 133
Score = 62.4 bits (152), Expect = 1e-11
Identities = 34/148 (22%), Positives = 56/148 (37%), Gaps = 18/148 (12%)
Query: 69 SHILCVISEDKTLETVLTNTVGVAIVDLDTKKFYMGEIPDDDYYSNLEAIIVQKSPKECL 128
+++ + D N G+A +DL T +F + E D + L A + + SPKE L
Sbjct: 1 NYLAAISRGDG-------NRYGLAFLDLSTGEFGVSEFED---FEELLAELSRLSPKELL 50
Query: 129 LPAEYLNDNKNKIVTILDRNKVCMTGRKKNEFSEEDLMQDVNR-LVRFDDSELKNARLLP 187
LP + + +L+ R F E +D+N D L
Sbjct: 51 LPESLSSSTVAESQKLLELRLRV-GRRPTWLFELEHAYEDLNEDFGVEDLDGFGLEELPL 109
Query: 188 EMCLTTATHCLRSLINYLELMNNEDNMN 215
+C A LI+YL+ E+ +
Sbjct: 110 ALCAAGA------LISYLKETQKENLPH 131
>gnl|CDD|213179 cd00267, ABC_ATPase, ATP-binding cassette transporter
nucleotide-binding domain. ABC transporters are a large
family of proteins involved in the transport of a wide
variety of different compounds, like sugars, ions,
peptides, and more complex organic molecules. The
nucleotide-binding domain shows the highest similarity
between all members of the family. ABC transporters are
a subset of nucleotide hydrolases that contain a
signature motif, Q-loop, and H-loop/switch region, in
addition to, the Walker A motif/P-loop and Walker B
motif commonly found in a number of ATP- and GTP-binding
and hydrolyzing proteins.
Length = 157
Score = 51.9 bits (125), Expect = 1e-07
Identities = 31/157 (19%), Positives = 54/157 (34%), Gaps = 22/157 (14%)
Query: 535 QGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSIGVSVFLAQIGCFVPCDSATISV 594
G + + K+GE + GPN GKST +R I + S I +
Sbjct: 10 GGRTALDNVSLTLKAGE--IVALVGPNGSGKSTLLR---------AIAGLLKPTSGEILI 58
Query: 595 VDQIFTRVGAADSQYR-----GISTFMMEMKETATVIKKCTENSLVIIDELGRGTSTFDG 649
+ ++ + + R +S + A + L+++DE G
Sbjct: 59 DGKDIAKLPLEELRRRIGYVPQLSGGQRQRVALARAL--LLNPDLLLLDEPTSGLDPASR 116
Query: 650 FGMACSIARELASHRQPFTLFATHFHEIALLS--RVI 684
+ + R + TH E+A L+ RVI
Sbjct: 117 ERLLELLRELAEEGRT--VIIVTHDPELAELAADRVI 151
>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 = 46.1 bits (110), Expect = 3e-06
Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 4/88 (4%)
Query: 373 KMMDRKDAVMDKMKEYLESTARRLNLVADKTIKLENSPQ-GFAYRITMKLNNSIDDRYTI 431
++ D + + ++ E L RL + K++K+ + G+ +T + Y
Sbjct: 8 ELRDLLEELESELDELLAKERERLGI---KSLKVGYNKVFGYYIEVTRSEAKKVPKDYIR 64
Query: 432 LDTVRGGVRFQDDRLATANTQYQAIQRE 459
T++ GVRF L + + E
Sbjct: 65 RQTLKNGVRFTTPELKKLEDELLEAEEE 92
>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 = 35.6 bits (83), Expect = 0.019
Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 4/52 (7%)
Query: 2 KFYLFFFPQKSKTTIRFFNRVEFYCVHGEDAELIQRKSNVVYLVKTMGQKDK 53
+ Y K + FF +FY + GEDAE+ R + + T+
Sbjct: 5 RQY-LELKSKYPDAVLFFRVGDFYELFGEDAEIAAR---ELGITLTVRGGGS 52
>gnl|CDD|223668 COG0595, COG0595, mRNA degradation ribonucleases J1/J2
(metallo-beta-lactamase superfamily) [Translation,
ribosomal structure and biogenesis; Replication,
recombination and repair].
Length = 555
Score = 33.8 bits (78), Expect = 0.44
Identities = 30/139 (21%), Positives = 51/139 (36%), Gaps = 16/139 (11%)
Query: 359 ASNLNTILSSLQSLKMMDRKDAVMDKMKEYLESTARRLNLVADKTIKLENSPQGFAYRIT 418
ASN+ I + + + + + RK V + E L + ARRL + P I
Sbjct: 235 ASNIERIQTIIDAAEKLGRKVVVTGRSMERLIAIARRLGYL--------KLPDESFIEIR 286
Query: 419 MKLNNSIDDRYTILDTVRGGVRFQDD-RLATANTQYQAIQREYETHQQSIVEEVIGISAG 477
++ D+ I+ T G R+A +Y I +E +T S G
Sbjct: 287 -EVKRYPDEEVLIICTGSQGEPMAALSRMANGEHRYVKI-KEGDTVIFSSS-----PIPG 339
Query: 478 YTQTLNQLSDVLAQFDVLV 496
+ +L + L + V
Sbjct: 340 NEAAVYRLLNRLYKAGAKV 358
>gnl|CDD|216923 pfam02190, LON, ATP-dependent protease La (LON) domain. This
domain has been shown to be part of the PUA superfamily.
Length = 191
Score = 32.4 bits (74), Expect = 0.56
Identities = 12/58 (20%), Positives = 23/58 (39%)
Query: 378 KDAVMDKMKEYLESTARRLNLVADKTIKLENSPQGFAYRITMKLNNSIDDRYTILDTV 435
+ V + +++ E L L I P A I L S +++ +L+T+
Sbjct: 119 EALVKELIEKIKELLPLLLPLELLLKIDDIEDPGRLADLIASLLPLSPEEKQELLETL 176
>gnl|CDD|226931 COG4565, CitB, Response regulator of citrate/malate metabolism
[Transcription / Signal transduction mechanisms].
Length = 224
Score = 32.2 bits (74), Expect = 0.84
Identities = 21/89 (23%), Positives = 37/89 (41%), Gaps = 20/89 (22%)
Query: 426 DDRYTILDTVRGGV------RFQDDRLATANTQYQAIQREYETHQ---QSIVEEVIGISA 476
D TI + +R GV F +RL A T+Y+ + E+HQ Q ++++ I +
Sbjct: 84 SDMETIKEALRYGVVDYLIKPFTFERLQQALTRYRQKRHALESHQQLSQKELDQLFNIQS 143
Query: 477 GYTQ-----------TLNQLSDVLAQFDV 494
TL ++ + L + D
Sbjct: 144 KEQPPDDLPKGLDELTLQKVREALKEPDQ 172
>gnl|CDD|113511 pfam04744, Monooxygenase_B, Monooxygenase subunit B protein.
Family of membrane associated monooxygenases (EC
1.13.12.-) which utilise O(2) to oxidise their
substrate. Family members include both ammonia and
methane monooxygenases involved in the oxidation of
their respective substrates. These enzymes are
multi-subunit complexes. This family represents the B
subunit of the enzyme; the A subunit is thought to
contain the active site..
Length = 381
Score = 32.5 bits (74), Expect = 1.0
Identities = 10/42 (23%), Positives = 21/42 (50%)
Query: 412 GFAYRITMKLNNSIDDRYTILDTVRGGVRFQDDRLATANTQY 453
G A R+T+++ N D+ + + G+RF + + + Y
Sbjct: 262 GRALRMTVEVTNHGDEPLRLGEFTTAGIRFLNSDVRKDDPGY 303
>gnl|CDD|213206 cd03239, ABC_SMC_head, The SMC head domain belongs to the
ATP-binding cassette superfamily. The structural
maintenance of chromosomes (SMC) proteins are essential
for successful chromosome transmission during
replication and segregation of the genome in all
organisms. SMCs are generally present as single proteins
in bacteria, and as at least six distinct proteins in
eukaryotes. The proteins range in size from
approximately 110 to 170 kDa, and each has five distinct
domains: amino- and carboxy-terminal globular domains,
which contain sequences characteristic of ATPases, two
coiled-coil regions separating the terminal domains ,
and a central flexible hinge. SMC proteins function
together with other proteins in a range of chromosomal
transactions, including chromosome condensation,
sister-chromatid cohesion, recombination, DNA repair,
and epigenetic silencing of gene expression.
Length = 178
Score = 31.5 bits (72), Expect = 1.1
Identities = 22/77 (28%), Positives = 32/77 (41%), Gaps = 15/77 (19%)
Query: 532 VELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSI-------------GVSVFL 578
+ L+ SY D G SFN + GPN GKS + +I G +FL
Sbjct: 4 ITLKNFKSY--RDETVVGGSNSFNAIVGPNGSGKSNIVDAICFVLGGKAAKLRRGSLLFL 61
Query: 579 AQIGCFVPCDSATISVV 595
A G +SA++ +
Sbjct: 62 AGGGVKAGINSASVEIT 78
>gnl|CDD|219836 pfam08429, PLU-1, PLU-1-like protein. Sequences in this family
bear similarity to the central region of PLU-1. This is
a nuclear protein that may have a role in DNA-binding
and transcription, and is closely associated with the
malignant phenotype of breast cancer. This region is
found in various other Jumonji/ARID domain-containing
proteins (see pfam02373, pfam01388).
Length = 335
Score = 31.5 bits (72), Expect = 1.9
Identities = 26/140 (18%), Positives = 49/140 (35%), Gaps = 26/140 (18%)
Query: 246 STSAQTYDSLLGILD---RCRTPQGHRLLA----------QWMKQ----------PLKDL 282
S A T D + ++D P + +A +W ++ L L
Sbjct: 176 SDPAMTLDDVRELIDEGVSLGPPSVEKAMAELQELLTKAEEWEEKAKELLSRPQHSLDTL 235
Query: 283 DAIVERHAAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDCYRVYEGVSQ 342
+A+++ + + + N + + A ++SL + GRK+ L + +
Sbjct: 236 EALIKEAENIPVSLPNLAKLKEILQKAREWQTQVESLLEQDGRKRPKLDELEELVAESEP 295
Query: 343 LPKLI---SILESLVQNVEA 359
LP LE V EA
Sbjct: 296 LPVKPEELRQLEKEVARAEA 315
>gnl|CDD|236790 PRK10901, PRK10901, 16S rRNA methyltransferase B; Provisional.
Length = 427
Score = 30.9 bits (71), Expect = 2.6
Identities = 16/58 (27%), Positives = 22/58 (37%), Gaps = 17/58 (29%)
Query: 262 CRT-PQGHRLLAQWMKQPLKDLDAIVER----------------HAAVNILVNNTEAR 302
R P+ L+AQ + +PLK IV HAAV+ V +A
Sbjct: 49 LRRLPRLEWLIAQLLAKPLKGKQRIVHALLLVGLYQLLYTRIPAHAAVDETVEAAKAL 106
>gnl|CDD|223047 PHA03332, PHA03332, membrane glycoprotein; Provisional.
Length = 1328
Score = 31.5 bits (71), Expect = 2.6
Identities = 25/118 (21%), Positives = 49/118 (41%), Gaps = 5/118 (4%)
Query: 374 MMDRKDAVMDKMKEYLESTARRLNLVADKTIKLENSPQGFAYRITMKLNNSIDDRYTILD 433
+ + A +M + R++ +D KL ++ +I+ L+N+I +
Sbjct: 885 QLLQATAATAEMASKIGGLNARVDKTSDVITKLGDT----IAKISATLDNNIRAVNGRVS 940
Query: 434 TVRGGVRFQDDRLATANTQYQAIQREYETHQQSIVEEVIGISAGYTQTLNQLSDVLAQ 491
+ V + +AT +E T +EEV+ +A Y Q LN L++ + Q
Sbjct: 941 DLEDQVNLRFLAVATNFNTLATQLKELGTTTNERIEEVMA-AALYYQQLNSLTNQVTQ 997
>gnl|CDD|213244 cd03277, ABC_SMC5_euk, ATP-binding cassette domain of eukaryotic
SMC5 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five recognizable
domains. Amino-acid sequence homology of SMC proteins
between species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 213
Score = 30.3 bits (69), Expect = 3.3
Identities = 21/74 (28%), Positives = 34/74 (45%), Gaps = 13/74 (17%)
Query: 532 VELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSI-----GVSVFL---AQIGC 583
++L+ V+Y + S N++ GPN GKS+ + +I G L ++G
Sbjct: 6 IKLENFVTYDETEFRPGP---SLNMIIGPNGSGKSSIVCAICLGLGGKPKLLGRAKKVGE 62
Query: 584 FVP--CDSATISVV 595
FV CD TI +
Sbjct: 63 FVKRGCDEGTIEIE 76
>gnl|CDD|237421 PRK13539, PRK13539, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 207
Score = 30.2 bits (69), Expect = 3.5
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 9/37 (24%)
Query: 543 NDVYFKSGEVSFNL-------VTGPNMGGKSTYIRSI 572
V F +SF L +TGPN GK+T +R I
Sbjct: 14 GRVLFSG--LSFTLAAGEALVLTGPNGSGKTTLLRLI 48
>gnl|CDD|227415 COG5083, SMP2, Uncharacterized protein involved in plasmid
maintenance [General function prediction only].
Length = 580
Score = 30.6 bits (69), Expect = 3.6
Identities = 16/91 (17%), Positives = 29/91 (31%), Gaps = 14/91 (15%)
Query: 735 RDLMKEYEYSLDTKTPSGDET--NNREEEYFKTVQEGEYQMFDFLQQC----------LS 782
+L+ SL E N RE+E + + FD + + S
Sbjct: 94 YELILSPNNSLTASPDQDPELILNEREQESLGSGSDLSKLNFDIVLKEPKNLDIGFRKYS 153
Query: 783 LSKQKDTNRILHLQE--TQEPGIEEYQSFDK 811
+K+ + + Q + Y F+K
Sbjct: 154 RNKRTENTGKRMYGQSSRQRGHKDSYHLFEK 184
>gnl|CDD|215357 PLN02665, PLN02665, pectinesterase family protein.
Length = 366
Score = 30.4 bits (69), Expect = 4.1
Identities = 16/51 (31%), Positives = 23/51 (45%), Gaps = 8/51 (15%)
Query: 285 IVERH--AAVNILVNNTEARMNLHEYALRGLPDMQSLAMRIGRKKAGLKDC 333
IVE A NI++ N+ R + Q++AMRI KA +C
Sbjct: 150 IVESDYFMAANIIIKNSAPRPD------GKRKGAQAVAMRISGDKAAFYNC 194
>gnl|CDD|239982 cd04609, CBS_pair_PALP_assoc2, This cd contains two tandem repeats
of the cystathionine beta-synthase (CBS pair) domains
associated with the pyridoxal-phosphate (PALP) dependent
enzyme domain upstream. The vitamin B6 complex
comprises pyridoxine, pyridoxal, and pyridoxamine, as
well as the 5'-phosphate esters of pyridoxal (PALP) and
pyridoxamine, the last two being the biologically active
coenzyme derivatives. The members of the PALP family
are principally involved in the biosynthesis of amino
acids and amino acid-derived metabolites, but they are
also found in the biosynthetic pathways of amino sugars
and other amine-containing compounds. CBS is a small
domain originally identified in cystathionine
beta-synthase and subsequently found in a wide range of
different proteins. CBS domains usually come in tandem
repeats, which associate to form a so-called Bateman
domain or a CBS pair which is reflected in this model.
The interface between the two CBS domains forms a cleft
that is a potential ligand binding site. The CBS pair
coexists with a variety of other functional domains. It
has been proposed that the CBS domain may play a
regulatory role, although its exact function is unknown.
Length = 110
Score = 28.7 bits (65), Expect = 4.4
Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 5/27 (18%)
Query: 718 VHCAKMAGYPEDMLEQARDLMKEYEYS 744
V A P+D + QA + M+EY S
Sbjct: 4 VSVA-----PDDTVSQAIERMREYGVS 25
>gnl|CDD|216304 pfam01113, DapB_N, Dihydrodipicolinate reductase, N-terminus.
Dihydrodipicolinate reductase (DapB) reduces the
alpha,beta-unsaturated cyclic imine,
dihydro-dipicolinate. This reaction is the second
committed step in the biosynthesis of L-lysine and its
precursor meso-diaminopimelate, which are critical for
both protein and cell wall biosynthesis. The N-terminal
domain of DapB binds the dinucleotide NADPH.
Length = 122
Score = 28.8 bits (65), Expect = 4.5
Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 4/61 (6%)
Query: 455 AIQREYETHQQSIVEEVIGISAGYTQTLNQLSDVLAQFDVLVSFSIASTCAPKPYVRPCM 514
A+ R + S E+ G + L +VLA DVL+ F+ A + +
Sbjct: 31 AVDRPGSSLLGSDAGELAGPLGVPVT--DDLEEVLADADVLIDFTTPE--ATLENLELAL 86
Query: 515 K 515
K
Sbjct: 87 K 87
>gnl|CDD|224046 COG1121, ZnuC, ABC-type Mn/Zn transport systems, ATPase component
[Inorganic ion transport and metabolism].
Length = 254
Score = 29.9 bits (68), Expect = 4.6
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 530 PIVELQG-GVSY----IPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSI 572
P++E++ VSY + D+ + + GPN GKST +++I
Sbjct: 3 PMIEVENLTVSYGNRPVLEDISLSVEKGEITALIGPNGAGKSTLLKAI 50
>gnl|CDD|223450 COG0373, HemA, Glutamyl-tRNA reductase [Coenzyme metabolism].
Length = 414
Score = 29.5 bits (67), Expect = 6.9
Identities = 16/57 (28%), Positives = 21/57 (36%), Gaps = 6/57 (10%)
Query: 20 NRVEFYCVHGEDAELIQRKSNVVYLVKTMGQKDKTLETVLVNKSNLSCFSHILCVIS 76
NRVE Y V +ELI+ L + G + L L H+ V S
Sbjct: 51 NRVEIYAVVHTGSELIRF------LAELHGLSIEDLGKYLYVLRGEEAVRHLFRVAS 101
>gnl|CDD|218494 pfam05201, GlutR_N, Glutamyl-tRNAGlu reductase, N-terminal
domain.
Length = 150
Score = 28.7 bits (65), Expect = 7.6
Identities = 16/57 (28%), Positives = 21/57 (36%), Gaps = 4/57 (7%)
Query: 20 NRVEFYCVHGEDAELIQRKSNVVYLVKTMGQKDKTLETVLVNKSNLSCFSHILCVIS 76
NRVE Y V DA + +L + G + LE L H+ V S
Sbjct: 46 NRVEIYAVVDHDASEDLIE----FLAELSGLDIEELEEYLYVYEGEEAVRHLFRVAS 98
>gnl|CDD|213202 cd03235, ABC_Metallic_Cations, ATP-binding cassette domain of the
metal-type transporters. This family includes
transporters involved in the uptake of various metallic
cations such as iron, manganese, and zinc. The ATPases
of this group of transporters are very similar to
members of iron-siderophore uptake family suggesting
that they share a common ancestor. The best
characterized metal-type ABC transporters are the
YfeABCD system of Y. pestis, the SitABCD system of
Salmonella enterica serovar Typhimurium, and the SitABCD
transporter of Shigella flexneri. Moreover other
uncharacterized homologs of these metal-type
transporters are mainly found in pathogens like
Haemophilus or enteroinvasive E. coli isolates.
Length = 213
Score = 29.0 bits (66), Expect = 8.6
Identities = 17/45 (37%), Positives = 23/45 (51%), Gaps = 10/45 (22%)
Query: 528 RHPIVELQGGVSYIPNDVYFKSGEVSFNLVTGPNMGGKSTYIRSI 572
HP++E VS K GE F + GPN GKST +++I
Sbjct: 11 GHPVLE---DVS-----FEVKPGE--FLAIVGPNGAGKSTLLKAI 45
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
0.319 0.134 0.381
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 40,111,919
Number of extensions: 3911431
Number of successful extensions: 3971
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3922
Number of HSP's successfully gapped: 53
Length of query: 813
Length of database: 10,937,602
Length adjustment: 105
Effective length of query: 708
Effective length of database: 6,280,432
Effective search space: 4446545856
Effective search space used: 4446545856
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 63 (27.9 bits)