RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2198
(279 letters)
>gnl|CDD|238543 cd01123, Rad51_DMC1_radA, Rad51_DMC1_radA,B. This group of
recombinases includes the eukaryotic proteins RAD51,
RAD55/57 and the meiosis-specific protein DMC1, and the
archaeal proteins radA and radB. They are closely
related to the bacterial RecA group. Rad51 proteins
catalyze a similiar recombination reaction as RecA,
using ATP-dependent DNA binding activity and a
DNA-dependent ATPase. However, this reaction is less
efficient and requires accessory proteins such as
RAD55/57 .
Length = 235
Score = 155 bits (393), Expect = 2e-46
Identities = 58/191 (30%), Positives = 91/191 (47%), Gaps = 12/191 (6%)
Query: 43 VSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKG----VLYIC 98
++TGS+ D +L GGI G ITE+ G G GKTQLC Q+ +++Q+ G +YI
Sbjct: 1 LTTGSKALDELLGGGIETGSITEIFGEFGSGKTQLCHQLAVTVQLPIELGGLEGKAVYID 60
Query: 99 TESVFPTARLAQLCELSPLAKPKCSDKIFITHCYEFIDLKRTLESQSGFIEN--KVGMIV 156
TE F RL Q+ E L + D I++ Y + LE + ++ +++
Sbjct: 61 TEGTFRPERLVQIAERFGLDPEEVLDNIYVARAYNSDHQLQLLEELEAILIESSRIKLVI 120
Query: 157 IDSIAGIFRNTYAEDKYVQ-RAHDMRDLAHYLHELSIKHRIVVICTNQVTS-----AMTH 210
+DS+ +FR + + R + L L L+ + + V+ TNQVT+ AM
Sbjct: 121 VDSVTALFRAEFDGRGELAERQQHLAKLLRTLKRLADEFNVAVVITNQVTARPDGAAMFG 180
Query: 211 SDKNIPALGLT 221
D PA G
Sbjct: 181 GDPKKPAGGNI 191
>gnl|CDD|238687 cd01393, recA_like, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to DNA
strand exchange. While prokaryotes have a single RecA
protein, eukaryotes have multiple RecA homologs such as
Rad51, DMC1 and Rad55/57. Archaea have the RecA-like
homologs radA and radB.
Length = 226
Score = 150 bits (382), Expect = 9e-45
Identities = 64/201 (31%), Positives = 91/201 (45%), Gaps = 19/201 (9%)
Query: 43 VSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKG----VLYIC 98
+STGS+ D +L GGI G ITE+ G G GKTQLCLQ+ + Q+ G V+YI
Sbjct: 1 ISTGSKALDELLGGGIPTGRITEIFGEFGSGKTQLCLQLAVEAQLPGELGGLEGKVVYID 60
Query: 99 TESVFPTARLAQLCELSPLAKPKCSDKIFITHCYEFIDLKRTLESQSGF-IENKVGMIVI 157
TE F RL QL L + D I++ Y +E +V ++V+
Sbjct: 61 TEGAFRPERLVQLAVRFGLDPEEVLDNIYVARPYNGEQQLEIVEELERIMSSGRVDLVVV 120
Query: 158 DSIAGIFRNTYAEDKYV-QRAHDMRDLAHYLHELSIKHRIVVICTNQVTS---AMTHSDK 213
DS+A +FR + + +RA + L L+ K + V+ TNQV + M +
Sbjct: 121 DSVAALFRKEFIGRGMLAERARLLSQALRKLLRLADKFNVAVVFTNQVRAKVDVMFGDPE 180
Query: 214 NIPALGLTYERAHDMRDLAHY 234
PA G LAH
Sbjct: 181 -TPAGGNA---------LAHA 191
>gnl|CDD|223544 COG0468, RecA, RecA/RadA recombinase [DNA replication,
recombination, and repair].
Length = 279
Score = 111 bits (281), Expect = 2e-29
Identities = 48/166 (28%), Positives = 71/166 (42%), Gaps = 14/166 (8%)
Query: 42 VVSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTES 101
+STGS D L GG+ G ITE+ G GKT L LQ+ + Q +P +I TE
Sbjct: 41 AISTGSLALDEALGGGLPRGRITEIYGPESSGKTTLALQLVANAQ--KPGGKAAFIDTEH 98
Query: 102 VFPTARLAQLCELSPLAKPKCSDKIFITHCYEFIDLKRTLESQSGFIENKVGMIVIDSIA 161
R QL D + ++ E + K+ ++V+DS+A
Sbjct: 99 ALDPERAKQLGV-------DLLDNLLVSQPDTGEQQLEIAEKLARSGAEKIDLLVVDSVA 151
Query: 162 GIFRNTYAEDKYVQRAHDMRDLAHYLHELSI---KHRIVVICTNQV 204
+ R ED ++ R L+ L +L+ K+ VI TNQV
Sbjct: 152 ALVRAEEIEDGHLGLRA--RLLSKALRKLTRLANKYNTAVIFTNQV 195
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 98.8 bits (247), Expect = 7e-25
Identities = 49/167 (29%), Positives = 81/167 (48%), Gaps = 11/167 (6%)
Query: 43 VSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTESV 102
+ TG + D +L GG G IT++ G G GKT +CLQ L+++ ++ K V+YI TE +
Sbjct: 5 LPTGCKMLDELLGGGFERGTITQIYGPPGSGKTNICLQ--LAVEAAKNGKKVIYIDTEGL 62
Query: 103 FPTARLAQLCELSPLAKPKCSDKIFITHCYEFIDLKRTLESQSGFIENKVGMIVIDSIAG 162
P R Q+ + I I F + + + VG+IV+DS
Sbjct: 63 SPE-RFKQIAGEDF---EELLSNIIIFEPSSFEEQSEAIRKAEKLAKENVGLIVLDSATS 118
Query: 163 IFRNTYAEDKYVQRAHDMRDLA---HYLHELSIKHRIVVICTNQVTS 206
++R +++ + R+L +L +L+ KH + V+ TNQV S
Sbjct: 119 LYRLELEDEEDNSKL--NRELGRQLTHLLKLARKHDLAVVITNQVYS 163
>gnl|CDD|185407 PTZ00035, PTZ00035, Rad51 protein; Provisional.
Length = 337
Score = 97.4 bits (243), Expect = 2e-23
Identities = 62/212 (29%), Positives = 93/212 (43%), Gaps = 21/212 (9%)
Query: 11 GFQEWEVNKVKDLKKK---KAFQVGKNPIDMTE--IVVSTGSEKFDSILKGGIHAGGITE 65
G E +V K+K+ K F ++ + I ++TGS + D +L GGI G ITE
Sbjct: 63 GISEAKVEKIKEAASKLVPMGFISATEYLEARKNIIRITTGSTQLDKLLGGGIETGSITE 122
Query: 66 LSGASGCGKTQLCLQMCLSLQVSQPHKG----VLYICTESVFPTARLAQLCELSPLAKPK 121
L G GKTQLC +C++ Q+ G VLYI TE F R+ Q+ E L
Sbjct: 123 LFGEFRTGKTQLCHTLCVTCQLPIEQGGGEGKVLYIDTEGTFRPERIVQIAERFGLDPED 182
Query: 122 CSDKIFITHCYEFIDLKRTLESQSG-FIENKVGMIVIDSIAGIFRNTY------AEDKYV 174
D I Y + L + E + ++++DS +FR Y AE
Sbjct: 183 VLDNIAYARAYNHEHQMQLLSQAAAKMAEERFALLIVDSATALFRVDYSGRGELAE---- 238
Query: 175 QRAHDMRDLAHYLHELSIKHRIVVICTNQVTS 206
R + L +L+ + + V+ TNQV +
Sbjct: 239 -RQQHLGKFLRALQKLADEFNVAVVITNQVMA 269
>gnl|CDD|117002 pfam08423, Rad51, Rad51. Rad51 is a DNA repair and recombination
protein and is a homologue of the bacterial ATPase RecA
protein.
Length = 261
Score = 89.3 bits (222), Expect = 5e-21
Identities = 49/176 (27%), Positives = 82/176 (46%), Gaps = 14/176 (7%)
Query: 41 IVVSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKG----VLY 96
I ++TGS++ D +L GGI G ITE+ G GKTQLC +C++ Q+ G LY
Sbjct: 23 IRITTGSKELDKLLGGGIETGSITEVFGEFRTGKTQLCHTLCVTCQLPLEMGGGEGKALY 82
Query: 97 ICTESVFPTARLAQLCELSPLAKPKCSDKIFITHCYEFIDLKRTLESQSG-FIENKVGMI 155
I TE F R+ + E L + D I Y + L + E++ ++
Sbjct: 83 IDTEGTFRPERIVAIAERFGLDPEEVLDNIAYARAYNTEHQMQLLLQAAAMMSESRFALL 142
Query: 156 VIDSIAGIFRNTYA-----EDKYVQRAHDMRDLAHYLHELSIKHRIVVICTNQVTS 206
++DS ++R ++ ++ A +R L L+ + + V+ TNQV +
Sbjct: 143 IVDSATALYRTDFSGRGELAERQQHLAKFLRSLQR----LADEFGVAVVITNQVVA 194
>gnl|CDD|238688 cd01394, radB, RadB. The archaeal protein radB shares similarity
radA, the archaeal functional homologue to the bacterial
RecA. The precise function of radB is unclear.
Length = 218
Score = 87.9 bits (218), Expect = 7e-21
Identities = 47/167 (28%), Positives = 81/167 (48%), Gaps = 11/167 (6%)
Query: 43 VSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTESV 102
+ TG + D +L GG+ G +T++ G G GKT + +Q L+++ + K V YI TE +
Sbjct: 1 LPTGCKGLDELLGGGVERGTVTQVYGPPGTGKTNIAIQ--LAVETAGQGKKVAYIDTEGL 58
Query: 103 FPTARLAQLCELSPLAKPKCSDKIFITHCYEFIDLKRTLESQSGFIENKVGMIVIDSIAG 162
R Q+ P + + I + +F + R ++ F + KV ++V+DS
Sbjct: 59 SS-ERFRQIAGDRP---ERAASSIIVFEPMDFNEQGRAIQETETFADEKVDLVVVDSATA 114
Query: 163 IFRNTYAEDKYVQRAHDMRDLAH---YLHELSIKHRIVVICTNQVTS 206
++R + R+LA +L L+ KH + V+ TNQV S
Sbjct: 115 LYR--LELGDDDTTIKNYRELAKQLTFLLWLARKHDVAVVITNQVYS 159
>gnl|CDD|235273 PRK04301, radA, DNA repair and recombination protein RadA;
Validated.
Length = 317
Score = 88.4 bits (220), Expect = 2e-20
Identities = 53/180 (29%), Positives = 85/180 (47%), Gaps = 25/180 (13%)
Query: 43 VSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKG----VLYIC 98
++TGS++ D +L GGI ITE G G GKTQ+C Q+ +++Q+ + G +YI
Sbjct: 84 ITTGSKELDELLGGGIETQSITEFYGEFGSGKTQICHQLAVNVQLPEEKGGLEGKAVYID 143
Query: 99 TESVFPTARLAQLCELSPLAKPKCSDKIFITHCYE------FIDLKRTLESQSGFIENKV 152
TE F R+ Q+ E L + D I + Y + L + +
Sbjct: 144 TEGTFRPERIEQMAEALGLDPDEVLDNIHVARAYNSDHQMLLAEKAEELIKE----GENI 199
Query: 153 GMIVIDSIAGIFRNTYAEDKYVQR---AHDMRDLAHYLHEL---SIKHRIVVICTNQVTS 206
++++DS+ FR AE YV R A + L +LH+L + + V+ TNQV +
Sbjct: 200 KLVIVDSLTAHFR---AE--YVGRGNLAERQQKLNKHLHDLLRLADLYNAAVVVTNQVMA 254
>gnl|CDD|131292 TIGR02238, recomb_DMC1, meiotic recombinase Dmc1. This model
describes DMC1, a subfamily of a larger family of DNA
repair and recombination proteins. It is eukaryotic only
and most closely related to eukaryotic RAD51. It also
resembles archaeal RadA (TIGR02236) and RadB (TIGR02237)
and bacterial RecA (TIGR02012). It has been
characterized for human as a recombinase active only in
meiosis.
Length = 313
Score = 87.9 bits (218), Expect = 4e-20
Identities = 58/212 (27%), Positives = 95/212 (44%), Gaps = 21/212 (9%)
Query: 11 GFQEWEVNKVKDLKKK---KAFQVGKNPIDMTEIV--VSTGSEKFDSILKGGIHAGGITE 65
G E +V+K+K+ K F + V ++TGS+ D IL GGI + ITE
Sbjct: 41 GLSEAKVDKIKEAASKIINPGFITAFEISQKRKKVLKITTGSQALDGILGGGIESMSITE 100
Query: 66 LSGASGCGKTQLCLQMCLSLQVSQPHKG----VLYICTESVFPTARLAQLCELSPLAKPK 121
+ G CGKTQL +C++ Q+ + G V YI TE F R+ + E +
Sbjct: 101 VFGEFRCGKTQLSHTLCVTAQLPREMGGGNGKVAYIDTEGTFRPDRIRAIAERFGVDPDA 160
Query: 122 CSDKIFIT------HCYEFIDLKRTLESQSGFIENKVGMIVIDSIAGIFRNTYA-EDKYV 174
D I H E +D + F E ++++DSI +FR ++ +
Sbjct: 161 VLDNILYARAYTSEHQMELLD-----YLAAKFSEEPFRLLIVDSIMALFRVDFSGRGELS 215
Query: 175 QRAHDMRDLAHYLHELSIKHRIVVICTNQVTS 206
+R + + L+++S + + V TNQV +
Sbjct: 216 ERQQKLAQMLSRLNKISEEFNVAVFVTNQVQA 247
>gnl|CDD|233794 TIGR02239, recomb_RAD51, DNA repair protein RAD51. This eukaryotic
sequence family consists of RAD51, a protein involved in
DNA homologous recombination and repair. It is similar
in sequence the exclusively meiotic recombinase DMC1
(TIGR02238), to archaeal families RadA (TIGR02236) and
RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Length = 316
Score = 86.7 bits (215), Expect = 8e-20
Identities = 48/176 (27%), Positives = 82/176 (46%), Gaps = 14/176 (7%)
Query: 41 IVVSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKG----VLY 96
I ++TGS++ D +L GGI G ITE+ G GKTQLC + ++ Q+ G LY
Sbjct: 76 IQLTTGSKELDKLLGGGIETGSITEIFGEFRTGKTQLCHTLAVTCQLPIDQGGGEGKALY 135
Query: 97 ICTESVFPTARLAQLCELSPLAKPKCSDKIFITHCYEFIDLKRTLESQSGFI-ENKVGMI 155
I TE F RL + E L D + Y + L+ + + E++ ++
Sbjct: 136 IDTEGTFRPERLLAIAERYGLNPEDVLDNVAYARAYNTDHQLQLLQQAAAMMSESRFALL 195
Query: 156 VIDSIAGIFRNTYA-----EDKYVQRAHDMRDLAHYLHELSIKHRIVVICTNQVTS 206
++DS ++R ++ + + A +R L L+ + + V+ TNQV +
Sbjct: 196 IVDSATALYRTDFSGRGELSARQMHLARFLRS----LQRLADEFGVAVVITNQVVA 247
>gnl|CDD|178728 PLN03186, PLN03186, DNA repair protein RAD51 homolog; Provisional.
Length = 342
Score = 85.6 bits (212), Expect = 3e-19
Identities = 57/209 (27%), Positives = 92/209 (44%), Gaps = 15/209 (7%)
Query: 11 GFQEWEVNKVKDLKKK-------KAFQVGKNPIDMTEIVVSTGSEKFDSILKGGIHAGGI 63
G E +V K+ + K A Q+ ++ I ++TGS + D IL+GGI G I
Sbjct: 68 GISEAKVEKILEAASKLVPLGFTTASQLHAQRQEI--IQITTGSRELDKILEGGIETGSI 125
Query: 64 TELSGASGCGKTQLCLQMCLSLQVSQPHKG----VLYICTESVFPTARLAQLCELSPLAK 119
TE+ G GKTQLC +C++ Q+ G +YI TE F RL Q+ E L
Sbjct: 126 TEIYGEFRTGKTQLCHTLCVTCQLPLDQGGGEGKAMYIDTEGTFRPQRLIQIAERFGLNG 185
Query: 120 PKCSDKIFITHCYEFIDLKRTL-ESQSGFIENKVGMIVIDSIAGIFRNTY-AEDKYVQRA 177
+ + Y L E+ S E + ++++DS ++R + + R
Sbjct: 186 ADVLENVAYARAYNTDHQSELLLEAASMMAETRFALMIVDSATALYRTEFSGRGELSARQ 245
Query: 178 HDMRDLAHYLHELSIKHRIVVICTNQVTS 206
+ L L+ + + V+ TNQV +
Sbjct: 246 MHLGKFLRSLQRLADEFGVAVVITNQVVA 274
>gnl|CDD|131290 TIGR02236, recomb_radA, DNA repair and recombination protein RadA.
This family consists exclusively of archaeal RadA
protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239), and archaeal RadB
(TIGR02237). This protein is involved in DNA repair and
recombination. The member from Pyrococcus horikoshii
contains an intein [DNA metabolism, DNA replication,
recombination, and repair].
Length = 310
Score = 84.8 bits (210), Expect = 4e-19
Identities = 52/196 (26%), Positives = 92/196 (46%), Gaps = 24/196 (12%)
Query: 22 DLKKKKAFQVGKNPIDMTEIVVSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQM 81
D+ +++ +GK ++TGS++ D +L GGI ITE+ G G GKTQ+C Q+
Sbjct: 66 DVLERRK-TIGK---------ITTGSKELDELLGGGIETQAITEVFGEFGSGKTQICHQL 115
Query: 82 CLSLQVSQPHKG----VLYICTESVFPTARLAQLCELSPLAKPKCSDKIFITHCYE---- 133
+++Q+ + G +YI TE+ F R+ Q+ E L + I++ Y
Sbjct: 116 AVNVQLPEEKGGLGGKAVYIDTENTFRPERIMQMAEARGLDPDEVLKNIYVARAYNSNHQ 175
Query: 134 --FIDLKRTLESQSGFIENKVGMIVIDSIAGIFRNTY-AEDKYVQRAHDMRDLAHYLHEL 190
++ L + + N V ++++DS+ FR Y +R + H L L
Sbjct: 176 MLLVEKAEDLIKE---LNNPVKLLIVDSLTSHFRAEYVGRGALAERQQKLNKHLHDLLRL 232
Query: 191 SIKHRIVVICTNQVTS 206
+ + V+ TNQV +
Sbjct: 233 ADLYNAAVVVTNQVMA 248
>gnl|CDD|233793 TIGR02237, recomb_radB, DNA repair and recombination protein RadB.
This family consists exclusively of archaeal RadB
protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
archaeal RadA (TIGR02236).
Length = 209
Score = 79.0 bits (195), Expect = 1e-17
Identities = 43/155 (27%), Positives = 76/155 (49%), Gaps = 8/155 (5%)
Query: 51 DSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTESVFPTARLAQ 110
D +L GG+ G IT++ G G GKT +C+ L++ ++ K V+YI TE R Q
Sbjct: 2 DELLGGGVERGTITQIYGPPGSGKTNICMI--LAVNAARQGKKVVYIDTEG-LSPERFKQ 58
Query: 111 LCELSPLAKPKCSDKIFITHCYEFIDLKRTLESQSGFIE-NKVGMIVIDSIAGIFRNTYA 169
+ E P + + ++F + ++ S FI+ + ++V+DS ++R +
Sbjct: 59 IAEDRP---ERALSNFIVFEVFDFDEQGVAIQKTSKFIDRDSASLVVVDSFTALYRLELS 115
Query: 170 EDKYVQRAHDMRDLAHYLHELSIKHRIVVICTNQV 204
+D+ + R L L L+ K + V+ TNQV
Sbjct: 116 DDRISRNRELARQLTL-LLSLARKKNLAVVITNQV 149
>gnl|CDD|215620 PLN03187, PLN03187, meiotic recombination protein DMC1 homolog;
Provisional.
Length = 344
Score = 76.4 bits (188), Expect = 5e-16
Identities = 53/207 (25%), Positives = 91/207 (43%), Gaps = 11/207 (5%)
Query: 11 GFQEWEVNKVKDLKKK---KAFQVGKNPIDMTEIVV--STGSEKFDSILKGGIHAGGITE 65
G E +V+K+ + +K + F G + + + VV +TGS+ D +L GGI ITE
Sbjct: 71 GLSEAKVDKICEAAEKLLNQGFITGSDALLKRKSVVRITTGSQALDELLGGGIETRCITE 130
Query: 66 LSGASGCGKTQLCLQMCLSLQVSQPHKG----VLYICTESVFPTARLAQLCELSPLAKPK 121
G GKTQL +C++ Q+ G V YI TE F R+ + E +
Sbjct: 131 AFGEFRSGKTQLAHTLCVTTQLPTEMGGGNGKVAYIDTEGTFRPDRIVPIAERFGMDADA 190
Query: 122 CSDKIFITHCYEFIDLKRTLESQSG-FIENKVGMIVIDSIAGIFRNTY-AEDKYVQRAHD 179
D I Y + L + E ++++DS+ +FR + + +R
Sbjct: 191 VLDNIIYARAYTYEHQYNLLLGLAAKMAEEPFRLLIVDSVIALFRVDFTGRGELAERQQK 250
Query: 180 MRDLAHYLHELSIKHRIVVICTNQVTS 206
+ + L +++ + + V TNQV +
Sbjct: 251 LAQMLSRLTKIAEEFNVAVYMTNQVIA 277
>gnl|CDD|223993 COG1066, Sms, Predicted ATP-dependent serine protease
[Posttranslational modification, protein turnover,
chaperones].
Length = 456
Score = 54.1 bits (131), Expect = 2e-08
Identities = 33/123 (26%), Positives = 54/123 (43%), Gaps = 17/123 (13%)
Query: 43 VSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTE-S 101
+STG E+ D +L GG+ G + + G G GK+ L LQ+ L VLY+ E S
Sbjct: 75 ISTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRGK---VLYVSGEES 131
Query: 102 VFPTARLAQLCELSPLAKPKCSDKIFITHCYEFIDLKRTLESQSGFIENKVGMIVIDSIA 161
+ A L ++ +++ D+ LE + K ++VIDSI
Sbjct: 132 LQQIKLRADRLGLP-------TNNLYLLAETNLEDIIAELE------QEKPDLVVIDSIQ 178
Query: 162 GIF 164
++
Sbjct: 179 TLY 181
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a wide
variety of presumed DNA repair proteins.
Length = 154
Score = 47.3 bits (113), Expect = 1e-06
Identities = 33/169 (19%), Positives = 54/169 (31%), Gaps = 47/169 (27%)
Query: 43 VSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQP--------HKGV 94
+ ++KG + GG+T L+GA G GK+ L L + ++ +P V
Sbjct: 15 LDAPPPPLRWLVKGLLPRGGLTLLAGAPGTGKSTLALDLAAAVATGRPFLGPFPVEPGRV 74
Query: 95 LYICTESVFPTA--RLAQLCELSPLAKPKCSDKIFITHCYEFIDLKRTLESQSGFIENKV 152
LY+ E RL L LE G
Sbjct: 75 LYLDGEDSEAGLRRRLRALG--------------------------EALEEIEG-----P 103
Query: 153 GMIVIDSIAGIFRNTYAEDKYVQRAHDMRDLAHYLHELSIKHRIVVICT 201
++VID +A + E+ + L L L+ + V+
Sbjct: 104 DLVVIDPLASLLGG--DEN----DNAAVGALLAALDRLARRTGAAVLLV 146
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 46.3 bits (110), Expect = 6e-06
Identities = 15/41 (36%), Positives = 20/41 (48%)
Query: 41 IVVSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQM 81
+ TG D IL GG+ G + ++G G GKT LQ
Sbjct: 3 ERIPTGIPGLDEILGGGLPRGSVVLITGPPGTGKTIFALQF 43
>gnl|CDD|219158 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is
one of the Kai proteins among which direct
protein-protein association may be a critical process
in the generation of circadian rhythms in
cyanobacteria.
Length = 231
Score = 45.7 bits (109), Expect = 6e-06
Identities = 18/38 (47%), Positives = 21/38 (55%)
Query: 43 VSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQ 80
V TG D ILKGGI G + ++G G GKT LQ
Sbjct: 1 VPTGIPGLDEILKGGIPRGRVVLITGGPGTGKTIFGLQ 38
>gnl|CDD|238541 cd01121, Sms, Sms (bacterial radA) DNA repair protein. This protein
is not related to archael radA any more than is to other
RecA-like NTPases. Sms has a role in recombination and
recombinational repair and is responsible for the
stabilization or processing of branched DNA molecules.
Length = 372
Score = 44.9 bits (107), Expect = 2e-05
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 43 VSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTE 100
+ TG E+ D +L GG+ G + + G G GK+ L LQ ++ ++++ VLY+ E
Sbjct: 64 IPTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQ--VAARLAKRGGKVLYVSGE 119
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only detects
a fraction of this vast family. The poorly conserved
N-terminal helix is missing from the alignment.
Length = 148
Score = 42.7 bits (100), Expect = 3e-05
Identities = 26/143 (18%), Positives = 43/143 (30%), Gaps = 20/143 (13%)
Query: 61 GGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTESVFPTARLAQLCELSPLAKP 120
G + + G G GKT L + L P GV+YI E + L +
Sbjct: 2 GEVILIVGPPGSGKTTLARALARELG--PPGGGVIYIDGEDILEEVLDQLLLIIVG---- 55
Query: 121 KCSDKIFITHCYEFIDLKRTLESQSGFIENKVGMIVIDSIAGIFRNTYAEDKYVQRAHDM 180
K + + K ++++D I T D + +
Sbjct: 56 --GKKASGSGELRLRLALALAR------KLKPDVLILDEI------TSLLDAEQEALLLL 101
Query: 181 RDLAHYLHELSIKHRIVVICTNQ 203
+ L L + + VI T
Sbjct: 102 LEELRLLLLLKSEKNLTVILTTN 124
>gnl|CDD|236994 PRK11823, PRK11823, DNA repair protein RadA; Provisional.
Length = 446
Score = 43.5 bits (104), Expect = 6e-05
Identities = 24/94 (25%), Positives = 39/94 (41%), Gaps = 10/94 (10%)
Query: 13 QEWEVNKVKDLKKKKAFQVGKNPIDMTEIV------VSTGSEKFDSILKGGIHAGGITEL 66
W N + + K +++I +STG + D +L GG+ G + +
Sbjct: 28 GAW--NTLVEEVAASKAGSSKPVQPLSDIEAEEEPRISTGIGELDRVLGGGLVPGSVVLI 85
Query: 67 SGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTE 100
G G GK+ L LQ+ L + VLY+ E
Sbjct: 86 GGDPGIGKSTLLLQVAARL--AAAGGKVLYVSGE 117
>gnl|CDD|238540 cd01120, RecA-like_NTPases, RecA-like NTPases. This family includes
the NTP binding domain of F1 and V1 H+ATPases, DnaB and
related helicases as well as bacterial RecA and related
eukaryotic and archaeal recombinases. This group also
includes bacterial conjugation proteins and related DNA
transfer proteins involved in type II and type IV
secretion.
Length = 165
Score = 40.9 bits (96), Expect = 2e-04
Identities = 35/172 (20%), Positives = 57/172 (33%), Gaps = 17/172 (9%)
Query: 63 ITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYI-CTESVFPTARLAQLCELSPLAKPK 121
+ + G +G GKT L LQ L+L ++ V+Y+ E + L
Sbjct: 1 LILVFGPTGSGKTTLALQ--LALNIATKGGKVVYVDIEEEIEELTERLIGESLKGAL--- 55
Query: 122 CSDKIFITHCYEFID-LKRTLESQSGFIEN-KVGMIVIDSIAGIFRNTYAEDKYVQR--A 177
D + I R L E +I++D + + R +
Sbjct: 56 --DNLIIVFATADDPAAARLLSKAERLRERGGDDLIILDELTRLVRALREIREGYPGELD 113
Query: 178 HDMRDLAHYLHELSIKHRIVVICTNQVTSAMTHSDKNIPALGLTYERAHDMR 229
++R+ L E + K + VI T QV S D + E D
Sbjct: 114 EELRE----LLERARKGGVTVIFTLQVPS-GDKGDPRLTRGAQNLEDIADTV 160
>gnl|CDD|225429 COG2874, FlaH, Predicted ATPases involved in biogenesis of archaeal
flagella [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 235
Score = 41.1 bits (97), Expect = 2e-04
Identities = 37/180 (20%), Positives = 73/180 (40%), Gaps = 26/180 (14%)
Query: 37 DMTE---IVVSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKG 93
M E ++ +G+++ D L GGI G + + G +G GK+ L + ++
Sbjct: 1 MMVEELKKIIKSGNDELDKRLGGGIPVGSLILIEGDNGTGKSVLSQRFAYGFLMNG--YR 58
Query: 94 VLYICTESVFPTAR--LAQLCELSPLAKPKCSD---KIFITHCYEFIDLKRT----LESQ 144
V Y+ TE T R + Q+ LS F + +R+ L+
Sbjct: 59 VTYVSTEL---TVREFIKQMESLSYDVSDFLLSGRLLFFPVNLEPVNWGRRSARKLLDLL 115
Query: 145 SGFIENK-VGMIVIDSIAGIFRNTYAEDKYVQRAHDMRDLAHYLHELSIKHRIVVICTNQ 203
FI+ +I+IDS++ TY + + + +L +LS +++++ +
Sbjct: 116 LEFIKRWEKDVIIIDSLSAFA--TYDSED------AVLNFMTFLRKLSDLGKVIILTVHP 167
>gnl|CDD|180381 PRK06067, PRK06067, flagellar accessory protein FlaH; Validated.
Length = 234
Score = 41.1 bits (97), Expect = 2e-04
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 42 VVSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTES 101
++STG+E+ D L GGI + + G G GK+ L Q + Q K V I TE+
Sbjct: 6 IISTGNEELDRKLGGGIPFPSLILIEGDHGTGKSVLSQQFVYGA-LKQGKK-VYVITTEN 63
>gnl|CDD|163593 TIGR03881, KaiC_arch_4, KaiC domain protein, PAE1156 family.
Members of this protein family are archaeal
single-domain KaiC_related proteins, homologous to the
Cyanobacterial circadian clock cycle protein KaiC, an
autokinase/autophosphorylase that has two copies of the
domain.
Length = 229
Score = 40.5 bits (95), Expect = 3e-04
Identities = 23/62 (37%), Positives = 31/62 (50%), Gaps = 4/62 (6%)
Query: 43 VSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLS-LQVSQPHKGVLYICTES 101
+STG E D +L+GGI G ++G G GKT CL L+ P V+Y+ TE
Sbjct: 2 LSTGVEGLDKLLEGGIPRGFFVAVTGEPGTGKTIFCLHFAYKGLRDGDP---VIYVTTEE 58
Query: 102 VF 103
Sbjct: 59 SR 60
>gnl|CDD|232966 TIGR00416, sms, DNA repair protein RadA. The gene protuct codes
for a probable ATP-dependent protease involved in both
DNA repair and degradation of proteins, peptides,
glycopeptides. Also known as sms. Residues 11-28 of the
SEED alignment contain a putative Zn binding domain.
Residues 110-117 of the seed contain a putative ATP
binding site both documented in Haemophilus and in
Listeria monocytogenes. for E.coli see ( J. BACTERIOL.
178:5045-5048(1996)) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 454
Score = 40.2 bits (94), Expect = 8e-04
Identities = 40/171 (23%), Positives = 65/171 (38%), Gaps = 26/171 (15%)
Query: 40 EIVVSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYIC- 98
S+G + D +L GGI G + + G G GK+ L LQ+ L +Q VLY+
Sbjct: 73 VPRFSSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKNQMK--VLYVSG 130
Query: 99 TESVFPTARLAQLCELSPLAKPKCSDKIFITHCYEFIDLKRTLESQSGFIENKVGMIVID 158
ES+ A L P +++ + + +E ++ VID
Sbjct: 131 EESLQQIKMRA-----IRLGLP--EPNLYVLSETNWEQICANIEEENPQA------CVID 177
Query: 159 SIAGIFRNTYAEDKYVQRA----HDMRDLAHYLHELSIKHRIVVICTNQVT 205
SI + Y+ D + A +R+ L L+ I + VT
Sbjct: 178 SI----QTLYSPD--ISSAPGSVSQVRECTAELMRLAKTRGIAIFIVGHVT 222
>gnl|CDD|236461 PRK09302, PRK09302, circadian clock protein KaiC; Reviewed.
Length = 509
Score = 40.2 bits (95), Expect = 9e-04
Identities = 18/36 (50%), Positives = 21/36 (58%)
Query: 45 TGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQ 80
TG E FD I GG+ G T +SG +G GKT LQ
Sbjct: 15 TGIEGFDDITHGGLPKGRPTLVSGTAGTGKTLFALQ 50
Score = 37.6 bits (88), Expect = 0.006
Identities = 16/38 (42%), Positives = 21/38 (55%)
Query: 40 EIVVSTGSEKFDSILKGGIHAGGITELSGASGCGKTQL 77
+S+G D +L GG G I +SGA+G GKT L
Sbjct: 252 NERISSGVPDLDEMLGGGFFRGSIILVSGATGTGKTLL 289
>gnl|CDD|200333 TIGR03878, thermo_KaiC_2, KaiC domain protein, AF_0795 family.
This KaiC domain-containing protein family occurs
sporadically across a broad taxonomic range
(Euryarchaeota, Aquificae, Dictyoglomi,
Epsilonproteobacteria, and Firmicutes), but exclusively
in thermophiles.
Length = 259
Score = 37.8 bits (88), Expect = 0.003
Identities = 32/120 (26%), Positives = 48/120 (40%), Gaps = 13/120 (10%)
Query: 56 GGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKG--VLYICTES--VFPTARLAQL 111
GGI A + ++G S GK+ + Q V Q +G VL++ ES F L
Sbjct: 31 GGIPAYSVINITGVSDTGKSLMVEQ----FAVKQASRGNPVLFVTVESPANFVVTSLKLR 86
Query: 112 CELSPLAKPKCSDKIFITHCYEFIDLKR---TLESQSGFI--ENKVGMIVIDSIAGIFRN 166
+ K D I + +L+ L + + E KV VIDSI G++
Sbjct: 87 ANAMGVDFEKIEDNIILIDAASSTELRENVPNLLATLAYAIKEYKVKNTVIDSITGLYEA 146
>gnl|CDD|131703 TIGR02655, circ_KaiC, circadian clock protein KaiC. Members of
this family are the circadian clock protein KaiC, part
of the kaiABC operon that controls circadian rhythm. It
may be universal in Cyanobacteria. Each member has two
copies of the KaiC domain (pfam06745), which is also
found in other proteins. KaiC performs
autophosphorylation and acts as its own transcriptional
repressor [Cellular processes, Other].
Length = 484
Score = 38.0 bits (88), Expect = 0.005
Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 8/63 (12%)
Query: 43 VSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTESV 102
+ T E FD I GG+ G T +SG SG GKT +Q + G+++ V
Sbjct: 3 IRTMIEGFDDISHGGLPIGRSTLVSGTSGTGKTLFSIQFL--------YNGIIHFDEPGV 54
Query: 103 FPT 105
F T
Sbjct: 55 FVT 57
Score = 29.1 bits (65), Expect = 2.6
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 43 VSTGSEKFDSILKGGIHAGGITELSGASGCGKTQL 77
VS+G + D + GG I +GA+G GKT L
Sbjct: 245 VSSGVVRLDEMCGGGFFKDSIILATGATGTGKTLL 279
>gnl|CDD|163589 TIGR03877, thermo_KaiC_1, KaiC domain protein, Ph0284 family.
Members of this family contain a single copy of the
KaiC domain (pfam06745) that occurs in two copies of
the circadian clock protein kinase KaiC itself. Members
occur primarily in thermophilic archaea and in
Thermotoga.
Length = 237
Score = 35.9 bits (83), Expect = 0.013
Identities = 16/38 (42%), Positives = 18/38 (47%)
Query: 43 VSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQ 80
V TG D IL GGI + LSG G GK+ Q
Sbjct: 3 VKTGIPGMDEILHGGIPERNVVLLSGGPGTGKSIFSQQ 40
>gnl|CDD|213227 cd03260, ABC_PstB_phosphate_transporter, ATP-binding cassette
domain of the phosphate transport system. Phosphate
uptake is of fundamental importance in the cell
physiology of bacteria because phosphate is required as
a nutrient. The Pst system of E. coli comprises four
distinct subunits encoded by the pstS, pstA, pstB, and
pstC genes. The PstS protein is a phosphate-binding
protein located in the periplasmic space. PstA and PstC
are hydrophobic and they form the transmembrane portion
of the Pst system. PstB is the catalytic subunit, which
couples the energy of ATP hydrolysis to the import of
phosphate across cellular membranes through the Pst
system, often referred as ABC-protein. PstB belongs to
one of the largest superfamilies of proteins
characterized by a highly conserved adenosine
triphosphate (ATP) binding cassette (ABC), which is
also a nucleotide binding domain (NBD).
Length = 227
Score = 36.0 bits (84), Expect = 0.013
Identities = 18/52 (34%), Positives = 22/52 (42%), Gaps = 5/52 (9%)
Query: 51 DSILKG---GIHAGGITELSGASGCGKTQL--CLQMCLSLQVSQPHKGVLYI 97
LK I G IT L G SGCGK+ L L L P +G + +
Sbjct: 13 KHALKDISLDIPKGEITALIGPSGCGKSTLLRLLNRLNDLIPGAPDEGEVLL 64
>gnl|CDD|235281 PRK04328, PRK04328, hypothetical protein; Provisional.
Length = 249
Score = 35.4 bits (82), Expect = 0.021
Identities = 16/38 (42%), Positives = 18/38 (47%)
Query: 43 VSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQ 80
V TG D IL GGI + LSG G GK+ Q
Sbjct: 5 VKTGIPGMDEILYGGIPERNVVLLSGGPGTGKSIFSQQ 42
>gnl|CDD|238483 cd00983, recA, RecA is a bacterial enzyme which has roles in
homologous recombination, DNA repair, and the induction
of the SOS response. RecA couples ATP hydrolysis to
DNA strand exchange.
Length = 325
Score = 35.3 bits (82), Expect = 0.024
Identities = 18/46 (39%), Positives = 20/46 (43%), Gaps = 1/46 (2%)
Query: 42 VVSTGSEKFDSILK-GGIHAGGITELSGASGCGKTQLCLQMCLSLQ 86
V+ TGS D L GG G I E+ G GKT L L Q
Sbjct: 35 VIPTGSLSLDIALGIGGYPKGRIIEIYGPESSGKTTLALHAIAEAQ 80
>gnl|CDD|236476 PRK09354, recA, recombinase A; Provisional.
Length = 349
Score = 34.0 bits (79), Expect = 0.069
Identities = 18/40 (45%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 42 VVSTGSEKFDSIL-KGGIHAGGITELSGASGCGKTQLCLQ 80
V+STGS D L GG+ G I E+ G GKT L L
Sbjct: 40 VISTGSLALDIALGIGGLPRGRIVEIYGPESSGKTTLALH 79
>gnl|CDD|223382 COG0305, DnaB, Replicative DNA helicase [DNA replication,
recombination, and repair].
Length = 435
Score = 33.4 bits (77), Expect = 0.11
Identities = 33/152 (21%), Positives = 54/152 (35%), Gaps = 30/152 (19%)
Query: 41 IVVSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTE 100
I V TG D I G G + ++ G GKT L L + L+ K V E
Sbjct: 177 IGVPTGFTDLDEIT-SGFRPGDLIIVAARPGMGKTALALNIALNAAADGR-KPVAIFSLE 234
Query: 101 SVFPTARLAQ--LCELS-----PLAKPKCSDKIF--ITHCYEFI-----------DLKRT 140
+L L S L + SD + + + L T
Sbjct: 235 --MSEEQLVMRLLSSESGIESSKLRTGRLSDDEWERLIKAASELSEAPIFIDDTPGLTIT 292
Query: 141 -LESQSG--FIENKVGMIVID---SIAGIFRN 166
+ S++ +++ +G+IVID + G ++
Sbjct: 293 EIRSKARRLKLKHNLGLIVIDYLQLMTGGKKS 324
>gnl|CDD|238542 cd01122, GP4d_helicase, GP4d_helicase is a homohexameric 5'-3'
helicases. Helicases couple NTP hydrolysis to the
unwinding of nucleic acid duplexes into their component
strands.
Length = 271
Score = 32.8 bits (75), Expect = 0.17
Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 2/53 (3%)
Query: 56 GGIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTE-SVFPTAR 107
G+ G + L+ +G GKT + L L ++Q V I E V TAR
Sbjct: 25 KGLRKGELIILTAGTGVGKTTFLREYALDL-ITQHGVRVGTISLEEPVVRTAR 76
>gnl|CDD|213222 cd03255, ABC_MJ0796_LolCDE_FtsE, ATP-binding cassette domain of the
transporters involved in export of lipoprotein and
macrolide, and cell division protein. This family is
comprised of MJ0796 ATP-binding cassette,
macrolide-specific ABC-type efflux carrier (MacAB), and
proteins involved in cell division (FtsE), and release
of lipoproteins from the cytoplasmic membrane (LolCDE).
They are clustered together phylogenetically. MacAB is
an exporter that confers resistance to macrolides, while
the LolCDE system is not a transporter at all. An FtsE
null mutants showed filamentous growth and appeared
viable on high salt medium only, indicating a role for
FtsE in cell division and/or salt transport. The LolCDE
complex catalyzes the release of lipoproteins from the
cytoplasmic membrane prior to their targeting to the
outer membrane.
Length = 218
Score = 32.1 bits (74), Expect = 0.21
Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 6/53 (11%)
Query: 53 ILKG---GIHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTESV 102
LKG I G + G SG GK+ L L + L + +P G + + +
Sbjct: 19 ALKGVSLSIEKGEFVAIVGPSGSGKSTL-LNI-LGG-LDRPTSGEVRVDGTDI 68
>gnl|CDD|162659 TIGR02012, tigrfam_recA, protein RecA. This model describes
orthologs of the recA protein. RecA promotes
hybridization of homolgous regions of DNA. A segment of
ssDNA can be hybridized to another ssDNA region, or to
a dsDNA region. ATP is hydrolyzed in the process. Part
of the SOS respones, it is regulated by LexA via
autocatalytic cleavage [DNA metabolism, DNA
replication, recombination, and repair].
Length = 321
Score = 32.3 bits (74), Expect = 0.22
Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 42 VVSTGSEKFDSILK-GGIHAGGITELSGASGCGKTQLCLQ 80
+STGS D L GG+ G I E+ G GKT L L
Sbjct: 35 TISTGSLSLDLALGVGGLPRGRIIEIYGPESSGKTTLALH 74
>gnl|CDD|163592 TIGR03880, KaiC_arch_3, KaiC domain protein, AF_0351 family.
This model represents a rather narrowly distributed
archaeal protein family in which members have a single
copy of the KaiC domain. This stands in contrast to the
circadian clock protein KaiC itself, with two copies of
the domain. Members are expected to have weak ATPase
activity, by homology to the
autokinase/autophosphorylase KaiC itself.
Length = 224
Score = 32.0 bits (73), Expect = 0.23
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 46 GSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQ 80
G D +L GG G + + G G GKT LQ
Sbjct: 1 GIPGLDEMLGGGFPEGHVIVVIGEYGTGKTTFSLQ 35
>gnl|CDD|213192 cd03225, ABC_cobalt_CbiO_domain1, First domain of the ATP-binding
cassette component of cobalt transport system. Domain
I of the ABC component of a cobalt transport family
found in bacteria, archaea, and eukaryota. The
transition metal cobalt is an essential component of
many enzymes and must be transported into cells in
appropriate amounts when needed. This ABC transport
system of the CbiMNQO family is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most of cobalt (Cbi)
transport systems possess a separate CbiN component,
the cobalt-binding periplasmic protein, and they are
encoded by the conserved gene cluster cbiMNQO. Both the
CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems.
Length = 211
Score = 31.3 bits (72), Expect = 0.34
Identities = 10/40 (25%), Positives = 16/40 (40%), Gaps = 3/40 (7%)
Query: 58 IHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYI 97
I G + G +G GK+ L + L P G + +
Sbjct: 24 IKKGEFVLIVGPNGSGKSTLLRLLNGLL---GPTSGEVLV 60
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 30.3 bits (69), Expect = 0.43
Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 3/56 (5%)
Query: 58 IHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTESVFPTARLAQLCE 113
GI L+G SG GKT L ++ L + V P L ++
Sbjct: 1 RRGAGIGVLTGESGSGKTTLLRRLARQL---PNRRVVYVEAPSLGTPKDLLRKILR 53
>gnl|CDD|234033 TIGR02857, CydD, thiol reductant ABC exporter, CydD subunit. The
gene pair cydCD encodes an ABC-family transporter in
which each gene contains an N-terminal membrane-spanning
domain (pfam00664) and a C-terminal ATP-binding domain
(pfam00005). In E. coli these genes were discovered as
mutants which caused the terminal heme-copper oxidase
complex cytochrome bd to fail to assemble. Recent work
has shown that the transporter is involved in export of
redox-active thiol compounds such as cysteine and
glutathione. The linkage to assembly of the cytochrome
bd complex is further supported by the conserved operon
structure found outside the gammaproteobacteria
(cydABCD) containing both the transporter and oxidase
genes components. The genes used as the seed members for
this model are all either found in the
gammproteobacterial context or the CydABCD context. All
members of this family scoring above trusted at the time
of its creation were from genomes which encode a
cytochrome bd complex. Unfortunately, the gene symbol
nomenclature adopted based on this operon in B. subtilis
assigns cydC to the third gene in the operon where this
gene is actually homologous to the E. coli cydD gene. We
have chosen to name all homologs in this family in
accordance with the precedence of publication of the E.
coli name, CydD.
Length = 529
Score = 31.5 bits (72), Expect = 0.54
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 3/40 (7%)
Query: 58 IHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYI 97
+ G L G SG GK+ L L + L P +G + +
Sbjct: 345 VPPGERVALVGPSGAGKSTL-LNLLLGF--VDPTEGSIAV 381
>gnl|CDD|233417 TIGR01447, recD, exodeoxyribonuclease V, alpha subunit. This
family describes the exodeoxyribonuclease V alpha
subunit, RecD. RecD is part of a RecBCD complex. A
related family in the Gram-positive bacteria separates
in a phylogenetic tree, has an additional N-terminal
extension of about 200 residues, and is not supported as
a member of a RecBCD complex by neighboring genes. The
related family is consequently described by a different
model [DNA metabolism, DNA replication, recombination,
and repair].
Length = 586
Score = 31.3 bits (71), Expect = 0.56
Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 6/54 (11%)
Query: 61 GGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTESVFPT----ARLAQ 110
+ ++G G GKT ++ L+L P +G L I + PT ARLA+
Sbjct: 160 SNFSLITGGPGTGKTTTVARLLLALVKQSPKQGKLRIALAA--PTGKAAARLAE 211
>gnl|CDD|215755 pfam00154, RecA, recA bacterial DNA recombination protein. RecA
is a DNA-dependent ATPase and functions in DNA repair
systems. RecA protein catalyzes an ATP-dependent DNA
strand-exchange reaction that is the central step in
the repair of dsDNA breaks by homologous recombination.
Length = 322
Score = 30.7 bits (70), Expect = 0.71
Identities = 18/40 (45%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 42 VVSTGSEKFDSIL-KGGIHAGGITELSGASGCGKTQLCLQ 80
V+STGS D L GG+ G I E+ G GKT L L
Sbjct: 32 VISTGSLGLDIALGIGGLPKGRIIEIYGPESSGKTTLALH 71
>gnl|CDD|181541 PRK08727, PRK08727, hypothetical protein; Validated.
Length = 233
Score = 30.2 bits (68), Expect = 0.84
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 66 LSGASGCGKTQLCLQMCLS 84
LSG +G GKT L L +C +
Sbjct: 46 LSGPAGTGKTHLALALCAA 64
>gnl|CDD|213226 cd03259, ABC_Carb_Solutes_like, ATP-binding cassette domain of the
carbohydrate and solute transporters-like. This family
is comprised of proteins involved in the transport of
apparently unrelated solutes and proteins specific for
di- and oligosaccharides and polyols. 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 = 213
Score = 30.2 bits (69), Expect = 0.92
Identities = 16/46 (34%), Positives = 22/46 (47%), Gaps = 3/46 (6%)
Query: 58 IHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTESVF 103
+ G L G SGCGKT L L++ L+ +P G + I V
Sbjct: 23 VEPGEFLALLGPSGCGKTTL-LRLIAGLE--RPDSGEILIDGRDVT 65
>gnl|CDD|213196 cd03229, ABC_Class3, ATP-binding cassette domain of the binding
protein-dependent transport systems. This class is
comprised of all BPD (Binding Protein Dependent)
systems that are largely represented in archaea and
eubacteria and are primarily involved in scavenging
solutes from the environment. 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 = 178
Score = 29.8 bits (68), Expect = 1.1
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 58 IHAGGITELSGASGCGKTQL 77
I AG I L G SG GK+ L
Sbjct: 23 IEAGEIVALLGPSGSGKSTL 42
>gnl|CDD|226361 COG3842, PotA, ABC-type spermidine/putrescine transport systems,
ATPase components [Amino acid transport and
metabolism].
Length = 352
Score = 29.9 bits (68), Expect = 1.5
Identities = 13/24 (54%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 58 IHAGGITELSGASGCGKTQLCLQM 81
I G L G SGCGKT L L+M
Sbjct: 28 IKKGEFVTLLGPSGCGKTTL-LRM 50
>gnl|CDD|224059 COG1136, SalX, ABC-type antimicrobial peptide transport system,
ATPase component [Defense mechanisms].
Length = 226
Score = 29.4 bits (67), Expect = 1.5
Identities = 13/46 (28%), Positives = 18/46 (39%), Gaps = 4/46 (8%)
Query: 36 IDMTEIVVSTGSEKFD-SILKG---GIHAGGITELSGASGCGKTQL 77
I++ + G LK I AG + G SG GK+ L
Sbjct: 2 IELKNVSKIYGLGGEKVEALKDVNLEIEAGEFVAIVGPSGSGKSTL 47
>gnl|CDD|213268 cd03301, ABC_MalK_N, The N-terminal ATPase domain of the maltose
transporter, MalK. ATP binding cassette (ABC) proteins
function from bacteria to human, mediating the
translocation of substances into and out of cells or
organelles. ABC transporters contain two
transmembrane-spanning domains (TMDs) or subunits and
two nucleotide binding domains (NBDs) or subunits that
couple transport to the hydrolysis of ATP. In the
maltose transport system, the periplasmic maltose
binding protein (MBP) stimulates the ATPase activity of
the membrane-associated transporter, which consists of
two transmembrane subunits, MalF and MalG, and two
copies of the ATP binding subunit, MalK, and becomes
tightly bound to the transporter in the catalytic
transition state, ensuring that maltose is passed to
the transporter as ATP is hydrolyzed.
Length = 213
Score = 29.1 bits (66), Expect = 1.8
Identities = 17/40 (42%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 58 IHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYI 97
I G L G SGCGKT L+M L+ +P G +YI
Sbjct: 23 IADGEFVVLLGPSGCGKTTT-LRMIAGLE--EPTSGRIYI 59
>gnl|CDD|235205 PRK04028, PRK04028, glutamyl-tRNA(Gln) amidotransferase subunit E;
Validated.
Length = 630
Score = 29.8 bits (68), Expect = 1.9
Identities = 15/45 (33%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 19 KVKD-LKKKKAFQVGKNPIDMTEIVVSTGSEKFDSILKGGIHAGG 62
K++D LK++ A V +D+TE+ T S I+K + GG
Sbjct: 265 KIRDELKERGAS-VEDEIVDVTELFKDTKS----KIIKKALKKGG 304
>gnl|CDD|223645 COG0572, Udk, Uridine kinase [Nucleotide transport and
metabolism].
Length = 218
Score = 29.2 bits (66), Expect = 1.9
Identities = 8/26 (30%), Positives = 14/26 (53%)
Query: 66 LSGASGCGKTQLCLQMCLSLQVSQPH 91
++G SG GKT + ++ L V +
Sbjct: 13 IAGGSGSGKTTVAKELSEQLGVEKVV 38
>gnl|CDD|213260 cd03293, ABC_NrtD_SsuB_transporters, ATP-binding cassette domain of
the nitrate and sulfonate transporters. NrtD and SsuB
are the ATP-binding subunits of the bacterial ABC-type
nitrate and sulfonate transport systems, respectively.
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 = 220
Score = 29.0 bits (66), Expect = 2.0
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 3/45 (6%)
Query: 58 IHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTESV 102
+ G L G SGCGK+ L L++ L+ +P G + + E V
Sbjct: 27 VEEGEFVALVGPSGCGKSTL-LRIIAGLE--RPTSGEVLVDGEPV 68
>gnl|CDD|213327 cd12119, ttLC_FACS_AlkK_like, Fatty acyl-CoA synthetases similar to
LC-FACS from Thermus thermophiles. This family includes
fatty acyl-CoA synthetases that can activate
medium-chain to long-chain fatty acids. They catalyze
the ATP-dependent acylation of fatty acids in a two-step
reaction. The carboxylate substrate first reacts with
ATP to form an acyl-adenylate intermediate, which then
reacts with CoA to produce an acyl-CoA ester. The fatty
acyl-CoA synthetases are responsible for fatty acid
degradation as well as physiological regulation of
cellular functions via the production of fatty acyl-CoA
esters. The fatty acyl-CoA synthetase from Thermus
thermophiles in this family was shown catalyzing the
long-chain fatty acid, myristoyl acid, while another
member in this family, the AlkK protein identified from
Pseudomonas oleovorans, targets medium chain fatty
acids. This family also includes uncharacterized FACS
proteins.
Length = 517
Score = 29.5 bits (67), Expect = 2.1
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 7/43 (16%)
Query: 162 GIFRNTYAEDKYVQRAHDMRDLAHYLHELSIK--HRIVVICTN 202
I R TYA+ + +R R LA+ L L +K R+ + N
Sbjct: 22 SIHRYTYAD--FYRRV---RRLANALESLGVKPGDRVATLAWN 59
>gnl|CDD|222264 pfam13614, AAA_31, AAA domain. This family includes a wide
variety of AAA domains including some that have lost
essential nucleotide binding residues in the P-loop.
Length = 145
Score = 28.7 bits (65), Expect = 2.1
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 2/32 (6%)
Query: 66 LSGASGCGKTQLCLQMCLSLQVSQPHKGVLYI 97
S G GKT L + SL ++ VLY+
Sbjct: 6 YSPVGGEGKTTFALNLAQSL--AEEGPKVLYL 35
>gnl|CDD|183226 PRK11607, potG, putrescine transporter ATP-binding subunit;
Provisional.
Length = 377
Score = 29.4 bits (66), Expect = 2.3
Identities = 17/36 (47%), Positives = 21/36 (58%), Gaps = 3/36 (8%)
Query: 58 IHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKG 93
I+ G I L GASGCGK+ L L+M + QP G
Sbjct: 42 IYKGEIFALLGASGCGKSTL-LRMLAGFE--QPTAG 74
>gnl|CDD|184128 PRK13541, PRK13541, cytochrome c biogenesis protein CcmA;
Provisional.
Length = 195
Score = 28.7 bits (64), Expect = 2.5
Identities = 22/68 (32%), Positives = 34/68 (50%), Gaps = 18/68 (26%)
Query: 63 ITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTESVFPTARLAQLCELSPLAKPKC 122
IT + GA+GCGK+ L L+M + QP G +Y + C ++ +AKP C
Sbjct: 28 ITYIKGANGCGKSSL-LRMIAGIM--QPSSGNIYY------------KNCNINNIAKPYC 72
Query: 123 SDKIFITH 130
+ +I H
Sbjct: 73 T---YIGH 77
>gnl|CDD|132027 TIGR02982, heterocyst_DevA, ABC exporter ATP-binding subunit,
DevA family. Members of this protein family are found
mostly in the Cyanobacteria, but also in the
Planctomycetes. Cyanobacterial examples are involved in
heterocyst formation, by which some fraction of members
of the colony undergo a developmental change and become
capable of nitrogen fixation. The DevBCA proteins are
thought export of either heterocyst-specific
glycolipids or an enzyme essential for formation of the
laminated layer found in heterocysts.
Length = 220
Score = 28.8 bits (65), Expect = 2.6
Identities = 11/20 (55%), Positives = 13/20 (65%)
Query: 58 IHAGGITELSGASGCGKTQL 77
I+ G I L+G SG GKT L
Sbjct: 28 INPGEIVILTGPSGSGKTTL 47
>gnl|CDD|131197 TIGR02142, modC_ABC, molybdenum ABC transporter, ATP-binding
protein. This model represents the ATP-binding
cassette (ABC) protein of the three subunit molybdate
ABC transporter. The three proteins of this complex are
homologous to proteins of the sulfate ABC transporter.
Molybdenum may be used in nitrogenases of
nitrogen-fixing bacteria and in molybdopterin
cofactors. In some cases, molybdate may be transported
by a sulfate transporter rather than by a specific
molybdate transporter [Transport and binding proteins,
Anions].
Length = 354
Score = 29.3 bits (66), Expect = 2.6
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 58 IHAGGITELSGASGCGKTQL 77
+ G+T + G SG GKT L
Sbjct: 20 LPGQGVTAIFGRSGSGKTTL 39
>gnl|CDD|237420 PRK13537, PRK13537, nodulation ABC transporter NodI; Provisional.
Length = 306
Score = 29.0 bits (65), Expect = 2.7
Identities = 18/45 (40%), Positives = 24/45 (53%), Gaps = 3/45 (6%)
Query: 66 LSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTESVFPTARLAQ 110
L G +G GKT L+M L L + P G + +C E V AR A+
Sbjct: 38 LLGPNGAGKTT-TLRMLLGL--THPDAGSISLCGEPVPSRARHAR 79
>gnl|CDD|223780 COG0708, XthA, Exonuclease III [DNA replication, recombination, and
repair].
Length = 261
Score = 28.7 bits (65), Expect = 3.1
Identities = 19/97 (19%), Positives = 37/97 (38%), Gaps = 25/97 (25%)
Query: 140 TLESQSGFIENKVGMIVIDSI---AGIFRNTYAEDKYVQRAHDMRDLAHYLHELSIKHRI 196
+ + IE + + ++ G ++ +K+ + + L +YL EL K +
Sbjct: 86 EDDEEGRVIEAEFDGFRVINLYFPNG---SSIGLEKFDYKLRFLDALRNYLEELLKKGKP 142
Query: 197 VVICTNQVTSAMTHSDKNIPALGLTYERAHDMRDLAH 233
VV+C D NI A + D+A+
Sbjct: 143 VVLC----------GDFNI---------APEEIDVAN 160
>gnl|CDD|227409 COG5077, COG5077, Ubiquitin carboxyl-terminal hydrolase
[Posttranslational modification, protein turnover,
chaperones].
Length = 1089
Score = 29.1 bits (65), Expect = 3.4
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 27 KAFQVGKNPIDMTEIVVSTGSEKFDSILKGGIH 59
Q G+ P+D TE+ S G + DS ++ I
Sbjct: 245 YNLQTGEEPVDTTELTRSFGWDSDDSFMQHDIQ 277
>gnl|CDD|224045 COG1120, FepC, ABC-type cobalamin/Fe3+-siderophores transport
systems, ATPase components [Inorganic ion transport and
metabolism / Coenzyme metabolism].
Length = 258
Score = 28.7 bits (65), Expect = 3.5
Identities = 15/57 (26%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 58 IHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTESV--FPTARLAQLC 112
I G IT + G +G GK+ L L+ L +P G + + + + LA+
Sbjct: 25 IPKGEITGILGPNGSGKSTL-LKCLAGLL--KPKSGEVLLDGKDIASLSPKELAKKL 78
>gnl|CDD|130262 TIGR01194, cyc_pep_trnsptr, cyclic peptide transporter. This model
describes cyclic peptide transporter in bacteria.
Bacteria have elaborate pathways for the production of
toxins and secondary metabolites. Many such compounds,
including syringomycin and pyoverdine are synthesized on
non-ribosomal templates consisting of a multienzyme
complex. On several occasions the proteins of the
complex and transporter protein are present on the same
operon. Often times these compounds cross the biological
membrane by specific transporters. Syringomycin is an
amphipathic, cylclic lipodepsipeptide when inserted into
host causes formation of channels, permeable to variety
of cations. On the other hand, pyoverdine is a cyclic
octa-peptidyl dihydroxyquinoline, which is efficient in
sequestering iron for uptake [Transport and binding
proteins, Amino acids, peptides and amines, Transport
and binding proteins, Other].
Length = 555
Score = 28.8 bits (64), Expect = 3.8
Identities = 20/87 (22%), Positives = 33/87 (37%), Gaps = 23/87 (26%)
Query: 21 KDLKKKKAFQVGKNPIDMTEIVVSTGSEKFDSILKGGIHAGGITELSGASGCGKTQLCLQ 80
K + + F +G PID+ I G I + G +GCGK+ L
Sbjct: 348 KAPEGSEGFALG--PIDLR------------------IAQGDIVFIVGENGCGKSTLAKL 387
Query: 81 MCLSLQVSQPHKGVLYICTESVFPTAR 107
C + P +G + + +V +R
Sbjct: 388 FC---GLYIPQEGEILLDGAAVSADSR 411
>gnl|CDD|130234 TIGR01166, cbiO, cobalt transport protein ATP-binding subunit.
This model describes the ATP binding subunit of the
multisubunit cobalt transporter in bacteria and its
equivalents in archaea. The model is restricted to ATP
subunit that is a part of the cobalt transporter, which
belongs to the ABC transporter superfamily (ATP Binding
Cassette). The model excludes ATP binding subunit that
are associated with other transporters belonging to ABC
transporter superfamily. This superfamily includes two
groups, one which catalyze the uptake of small
molecules, including ions from the external milieu and
the other group which is engaged in the efflux of small
molecular weight compounds and ions from within the
cell. Energy derived from the hydrolysis of ATP drive
the both the process of uptake and efflux [Transport
and binding proteins, Cations and iron carrying
compounds].
Length = 190
Score = 27.8 bits (62), Expect = 4.6
Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 3/37 (8%)
Query: 61 GGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYI 97
G + L GA+G GK+ L L + L +P G + I
Sbjct: 18 GEVLALLGANGAGKSTLLLHLNGLL---RPQSGAVLI 51
>gnl|CDD|213228 cd03261, ABC_Org_Solvent_Resistant, ATP-binding cassette
transport system involved in resistant to organic
solvents. 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 = 235
Score = 27.9 bits (63), Expect = 5.1
Identities = 14/45 (31%), Positives = 21/45 (46%), Gaps = 6/45 (13%)
Query: 36 IDMTEIVVSTGSEKFDSILKG---GIHAGGITELSGASGCGKTQL 77
I++ + S G +LKG + G I + G SG GK+ L
Sbjct: 1 IELRGLTKSFGGRT---VLKGVDLDVRRGEILAIIGPSGSGKSTL 42
>gnl|CDD|222864 PHA02542, 41, 41 helicase; Provisional.
Length = 473
Score = 28.1 bits (63), Expect = 5.1
Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 4/54 (7%)
Query: 48 EKFDSILKGGIHAGGITELSGASGCGKTQLCLQMC-LSLQVSQPHKGVLYICTE 100
E + I KGG + L GK+ L +C L+ Q VLYI E
Sbjct: 177 EILNKITKGGAERKTLNVLLAGVNVGKS---LGLCSLAADYLQQGYNVLYISME 227
>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 = 27.6 bits (62), Expect = 5.2
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 58 IHAGGITELSGASGCGKTQLCLQMCLSLQVSQ 89
+ AG I L G +G GK+ L + L+ +
Sbjct: 22 LKAGEIVALVGPNGSGKSTLLRAIAGLLKPTS 53
>gnl|CDD|226968 COG4615, PvdE, ABC-type siderophore export system, fused ATPase and
permease components [Secondary metabolites biosynthesis,
transport, and catabolism / Inorganic ion transport and
metabolism].
Length = 546
Score = 28.2 bits (63), Expect = 5.2
Identities = 12/40 (30%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 58 IHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYI 97
I G + L G +G GK+ L + L + QP G + +
Sbjct: 346 IKRGELVFLIGGNGSGKSTLAM---LLTGLYQPQSGEILL 382
>gnl|CDD|182181 PRK09983, pflD, putative formate acetyltransferase 2; Provisional.
Length = 765
Score = 28.2 bits (63), Expect = 5.7
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 7/82 (8%)
Query: 36 IDMTEIVV--STGSEKFDSILKGGIHA--GGITELSGASGCGKTQLCLQMCLSLQVSQPH 91
+ +IV+ ST S ++ + G A GG+TE ++ + LCL S+Q+ QP+
Sbjct: 302 VKCNDIVLLRSTSSARYFAGFPTGYTALLGGLTENGRSAVNVLSFLCLDAYQSVQLPQPN 361
Query: 92 KGVLYICTESVFPTARLAQLCE 113
GV T ++ T L + E
Sbjct: 362 LGVR---TNALIDTPFLMKTAE 380
>gnl|CDD|226963 COG4604, CeuD, ABC-type enterochelin transport system, ATPase
component [Inorganic ion transport and metabolism].
Length = 252
Score = 27.7 bits (62), Expect = 6.3
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 5/55 (9%)
Query: 58 IHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTESV--FPTARLAQ 110
I GGIT + G +G GK+ L M ++ + G + I + P+ LA+
Sbjct: 24 IPKGGITSIIGPNGAGKSTLLSMMS---RLLKKDSGEITIDGLELTSTPSKELAK 75
>gnl|CDD|234137 TIGR03176, AllC, allantoate amidohydrolase. This enzyme catalyzes
the breakdown of allantoate , first to ureidoglycine by
hydrolysis and then decarboxylation of one of the two
equivalent ureido groups. Ureidoglycine then
spontaneously exchanges ammonia for water resulting in
ureidoglycolate. This enzyme is an alternative to
allantoicase (3.5.3.4) which releases urea [Central
intermediary metabolism, Nitrogen metabolism].
Length = 406
Score = 27.9 bits (62), Expect = 6.7
Identities = 13/40 (32%), Positives = 18/40 (45%)
Query: 154 MIVIDSIAGIFRNTYAEDKYVQRAHDMRDLAHYLHELSIK 193
MI + SI GI N ++ LA L+EL+ K
Sbjct: 366 MIFVPSIGGISHNPAERTNIEDLVEGVKTLADMLYELAYK 405
>gnl|CDD|225246 COG2371, UreE, Urease accessory protein UreE [Posttranslational
modification, protein turnover, chaperones].
Length = 155
Score = 27.3 bits (61), Expect = 6.7
Identities = 16/61 (26%), Positives = 24/61 (39%), Gaps = 7/61 (11%)
Query: 170 EDKYVQRAHDMRDLAHYLHELSIKHRIVVICTNQVTSAMTHSDKNIPA----LGLTYERA 225
ED V RA +LA H L +H + +++ D + A LG+T R
Sbjct: 77 EDVLVIRAKTPLELAKAAHHLGNRHLPAQVEEDELR---VPYDHVLRAMLEGLGVTVTRV 133
Query: 226 H 226
Sbjct: 134 E 134
>gnl|CDD|213193 cd03226, ABC_cobalt_CbiO_domain2, Second domain of the
ATP-binding cassette component of cobalt transport
system. Domain II of the ABC component of a cobalt
transport family found in bacteria, archaea, and
eukaryota. The transition metal cobalt is an essential
component of many enzymes and must be transported into
cells in appropriate amounts when needed. The CbiMNQO
family ABC transport system is involved in cobalt
transport in association with the cobalamin (vitamin
B12) biosynthetic pathways. Most cobalt (Cbi) transport
systems possess a separate CbiN component, the
cobalt-binding periplasmic protein, and they are
encoded by the conserved gene cluster cbiMNQO. Both the
CbiM and CbiQ proteins are integral cytoplasmic
membrane proteins, and the CbiO protein has the linker
peptide and the Walker A and B motifs commonly found in
the ATPase components of the ABC-type transport
systems.
Length = 205
Score = 27.6 bits (62), Expect = 6.7
Identities = 14/38 (36%), Positives = 20/38 (52%), Gaps = 3/38 (7%)
Query: 43 VSTGSEKFDSILKG---GIHAGGITELSGASGCGKTQL 77
+S +K IL ++AG I L+G +G GKT L
Sbjct: 5 ISFSYKKGTEILDDLSLDLYAGEIIALTGKNGAGKTTL 42
>gnl|CDD|226970 COG4619, COG4619, ABC-type uncharacterized transport system, ATPase
component [General function prediction only].
Length = 223
Score = 27.5 bits (61), Expect = 7.3
Identities = 17/62 (27%), Positives = 26/62 (41%), Gaps = 3/62 (4%)
Query: 58 IHAGGITELSGASGCGKTQLCLQMCLSLQVSQPHKGVLYICTESVFPTARLAQLCELSPL 117
+ AG ++G SGCGK+ L + + P G L E V A ++S
Sbjct: 26 VRAGEFIAITGPSGCGKSTLLKIVAS---LISPTSGTLLFEGEDVSTLKPEAYRQQVSYC 82
Query: 118 AK 119
A+
Sbjct: 83 AQ 84
>gnl|CDD|182480 PRK10465, PRK10465, hydrogenase 2-specific chaperone; Provisional.
Length = 159
Score = 26.9 bits (60), Expect = 7.5
Identities = 10/30 (33%), Positives = 12/30 (40%)
Query: 66 LSGASGCGKTQLCLQMCLSLQVSQPHKGVL 95
LS G C +M LSL V+ P
Sbjct: 118 LSAEQGVRLADDCARMLLSLPVTNPDVPDA 147
>gnl|CDD|213968 TIGR04355, HprK_rel_B, HprK-related kinase B. Members of this
protein family resemble (and often are misannotated as)
HprK, the serine kinase/phosphatase of the
phosphocarrier protein HPr. However, members do not
occur with an HPr homolog, but instead as part of a
distinctive gene cassette of unknown function.
Length = 351
Score = 27.7 bits (62), Expect = 7.7
Identities = 11/29 (37%), Positives = 15/29 (51%), Gaps = 6/29 (20%)
Query: 59 HAGGITE------LSGASGCGKTQLCLQM 81
HA G+ L+G SG GK+ L L +
Sbjct: 148 HAAGVAHNGRGLALAGFSGMGKSTLALHL 176
>gnl|CDD|213218 cd03251, ABCC_MsbA, ATP-binding cassette domain of the bacterial
lipid flippase and related proteins, subfamily C. MsbA
is an essential ABC transporter, closely related to
eukaryotic MDR proteins. 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 = 234
Score = 27.2 bits (61), Expect = 7.7
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 58 IHAGGITELSGASGCGKTQLC 78
I AG L G SG GK+ L
Sbjct: 25 IPAGETVALVGPSGSGKSTLV 45
>gnl|CDD|223226 COG0148, Eno, Enolase [Carbohydrate transport and metabolism].
Length = 423
Score = 27.6 bits (62), Expect = 7.7
Identities = 16/56 (28%), Positives = 24/56 (42%), Gaps = 5/56 (8%)
Query: 146 GFIENKVGMIVIDSIAGIFRNTYAEDKYV--QRAHDMRDLAHYLHELSIKHRIVVI 199
G+ + + +D A F Y + KYV + +L Y EL K+ IV I
Sbjct: 229 GYEPGEDIALALDVAASEF---YKDGKYVLEGESLTSEELIEYYLELVKKYPIVSI 281
>gnl|CDD|213263 cd03296, ABC_CysA_sulfate_importer, ATP-binding cassette domain
of the sulfate transporter. Part of the ABC
transporter complex cysAWTP involved in sulfate import.
Responsible for energy coupling to the transport
system. The complex is composed of two ATP-binding
proteins (cysA), two transmembrane proteins (cysT and
cysW), and a solute-binding protein (cysP). 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 = 239
Score = 27.3 bits (61), Expect = 7.9
Identities = 10/20 (50%), Positives = 12/20 (60%)
Query: 58 IHAGGITELSGASGCGKTQL 77
I +G + L G SG GKT L
Sbjct: 25 IPSGELVALLGPSGSGKTTL 44
>gnl|CDD|213195 cd03228, ABCC_MRP_Like, ATP-binding cassette domain of multidrug
resistance protein-like transporters. The MRP
(Multidrug Resistance Protein)-like transporters are
involved in drug, peptide, and lipid export. They
belong to the subfamily C of the ATP-binding cassette
(ABC) superfamily of transport proteins. The ABCC
subfamily contains transporters with a diverse
functional spectrum that includes ion transport, cell
surface receptor, and toxin secretion activities. The
MRP-like family, similar to all ABC proteins, have a
common four-domain core structure constituted by two
membrane-spanning domains, each composed of six
transmembrane (TM) helices, and two nucleotide-binding
domains (NBD). 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 = 171
Score = 27.0 bits (61), Expect = 8.4
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 58 IHAGGITELSGASGCGKT 75
I G + G SG GK+
Sbjct: 25 IKPGEKVAIVGPSGSGKS 42
>gnl|CDD|213267 cd03300, ABC_PotA_N, ATP-binding cassette domain of the polyamine
transporter. PotA is an ABC-type transporter and the
ATPase component of the
spermidine/putrescine-preferential uptake system
consisting of PotA, -B, -C, and -D. PotA has two
domains with the N-terminal domain containing the
ATPase activity and the residues required for
homodimerization with PotA and heterdimerization with
PotB. 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 = 232
Score = 27.2 bits (61), Expect = 9.1
Identities = 11/20 (55%), Positives = 11/20 (55%)
Query: 58 IHAGGITELSGASGCGKTQL 77
I G L G SGCGKT L
Sbjct: 23 IKEGEFFTLLGPSGCGKTTL 42
>gnl|CDD|238544 cd01124, KaiC, KaiC is a circadian clock protein primarily found
in cyanobacteria KaiC is a RecA-like ATPase, having
both Walker A and Walker B motifs. A related protein is
found in archaea.
Length = 187
Score = 26.9 bits (60), Expect = 9.1
Identities = 10/21 (47%), Positives = 10/21 (47%)
Query: 63 ITELSGASGCGKTQLCLQMCL 83
T LSG G GKT LQ
Sbjct: 1 STLLSGGPGTGKTTFALQFLY 21
>gnl|CDD|146106 pfam03302, VSP, Giardia variant-specific surface protein.
Length = 397
Score = 27.2 bits (60), Expect = 9.9
Identities = 24/89 (26%), Positives = 32/89 (35%), Gaps = 20/89 (22%)
Query: 57 GIHAGGITELSGASGC-------GKTQLCLQMCLSLQVSQPHKGVLYICTESVFPTARLA 109
G G T +GA C T C + + P GV CT + AR
Sbjct: 143 GTCGEGCTTGTGAGACKTCGLTIDGTSYCSECATETEY--PQNGV---CTST---AARAT 194
Query: 110 QLCELSPLAKPKCS---DKIFITH--CYE 133
C+ S +A CS + F + CYE
Sbjct: 195 ATCKASSVANGMCSSCANGYFRMNGGCYE 223
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
0.321 0.135 0.405
Gapped
Lambda K H
0.267 0.0534 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,822,661
Number of extensions: 1275844
Number of successful extensions: 1620
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1580
Number of HSP's successfully gapped: 110
Length of query: 279
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 183
Effective length of database: 6,679,618
Effective search space: 1222370094
Effective search space used: 1222370094
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 (21.9 bits)
S2: 58 (26.6 bits)