RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3773
(578 letters)
>gnl|CDD|218689 pfam05681, Fumerase, Fumarate hydratase (Fumerase). This family
consists of several bacterial fumarate hydratase
proteins FumA and FumB. Fumarase, or fumarate hydratase
(EC 4.2.1.2), is a component of the citric acid cycle.
In facultative anaerobes such as Escherichia coli,
fumarase also engages in the reductive pathway from
oxaloacetate to succinate during anaerobic growth. Three
fumarases, FumA, FumB, and FumC, have been reported in
E. coli. fumA and fumB genes are homologous and encode
products of identical sizes which form thermolabile
dimers of Mr 120,000. FumA and FumB are class I enzymes
and are members of the iron-dependent hydrolases, which
include aconitase and malate hydratase. The active FumA
contains a 4Fe-4S centre, and it can be inactivated upon
oxidation to give a 3Fe-4S centre.
Length = 271
Score = 369 bits (951), Expect = e-125
Identities = 129/248 (52%), Positives = 165/248 (66%), Gaps = 14/248 (5%)
Query: 2 EKGIAAKDAIAQILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEG 61
E+ AK +AQIL N+ + A+ KRPICQDTG VF+KIG V G + + INEG
Sbjct: 31 EESPLAKFVLAQILENAEIAAEGKRPICQDTGTAVVFVKIGQEVPI---EGDLEEAINEG 87
Query: 62 VRRGYTNPNNILRASIVSDPHFIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKT 121
VRR YT LR S+V+DP RKNT DNTPAVI++E+VPG+ L+I +A+KGGGSENK+
Sbjct: 88 VRRAYTEGP--LRPSVVADP-LERKNTGDNTPAVIHIEIVPGDELEITVAAKGGGSENKS 144
Query: 122 KFAMLNPSD---SLVDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKVLMQDINM 178
K AMLNPSD + ++++TV G CPPG++G+GIGGT EKA L+AKK L++ ++
Sbjct: 145 KLAMLNPSDGIEGIKKFVLETVKEAGPNACPPGVVGVGIGGTSEKAALLAKKALLRPVDE 204
Query: 179 NSIIKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIP 238
+ P + EL EL KIN LGIG QG+GG +T LDVKI P H AS PVA+
Sbjct: 205 RN-----PDPRDAELEEELLEKINKLGIGPQGLGGKTTALDVKIERAPRHIASLPVAVNV 259
Query: 239 NCAATRHG 246
NC A RH
Sbjct: 260 NCWADRHA 267
>gnl|CDD|224862 COG1951, TtdA, Tartrate dehydratase alpha subunit/Fumarate
hydratase class I, N-terminal domain [Energy production
and conversion].
Length = 297
Score = 328 bits (843), Expect = e-109
Identities = 118/252 (46%), Positives = 155/252 (61%), Gaps = 13/252 (5%)
Query: 2 EKGIAAKDAIAQILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEG 61
E+ AK + QIL NSR+ AKE RPICQDTGI F+K+G G + + +NEG
Sbjct: 40 EESEIAKYVLLQILENSRIAAKENRPICQDTGIPIFFVKVGQRWPT---GGELEEALNEG 96
Query: 62 VRRGYTNPNNILRASIVSDPHFIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKT 121
VR +N LR S DP R NT DNTPA I++E+VPG+ ++I +A+KGGGSENK+
Sbjct: 97 VREAT--EDNPLRPSNAVDPLTKRVNTGDNTPAQIHVEIVPGDEVEILVAAKGGGSENKS 154
Query: 122 KFAMLNPSD---SLVDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKVLMQDINM 178
ML PS+ + D++++TV T+G CPP I+GIGIGGT EKA L+AKK L++ I+
Sbjct: 155 ALKMLTPSEGYEGIKDFVLETVRTLGGNACPPYIVGIGIGGTAEKAALLAKKALLRPIDD 214
Query: 179 NSIIKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIP 238
+ P K +L EL +IN LGIG QG+GG +T LDVK+ P H AS PVA+
Sbjct: 215 RN-----PNEKNAKLEEELLEEINKLGIGPQGLGGKTTALDVKVERAPRHPASLPVAVNV 269
Query: 239 NCAATRHGFLLF 250
C A R
Sbjct: 270 QCWADRRAKAKL 281
>gnl|CDD|180486 PRK06246, PRK06246, fumarate hydratase; Provisional.
Length = 280
Score = 270 bits (692), Expect = 9e-87
Identities = 116/247 (46%), Positives = 153/247 (61%), Gaps = 17/247 (6%)
Query: 6 AAKDAIAQILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRG 65
K+ + IL N+ + +E+ P+CQDTG+ VF++IG +V +G G + D INEGVR+G
Sbjct: 43 IGKEILKAILENAEIAKEEQVPLCQDTGMAVVFVEIGQDVHIEG--GDLEDAINEGVRKG 100
Query: 66 YTN-PNNILRASIVSDPHFIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKTKFA 124
Y LR S+V+DP RKNT DNTPAVI+ E+VPG+ L I +A KGGGSEN +
Sbjct: 101 YEEGY---LRKSVVADP-LTRKNTGDNTPAVIHTEIVPGDKLKITVAPKGGGSENMSALK 156
Query: 125 MLNPSDSL---VDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKVLMQDIN-MNS 180
ML P+D L ++++TV G CPP I+G+GIGGT +KA +AKK L++ I N
Sbjct: 157 MLKPADGLEGIKKFVLETVKEAGGNPCPPIIVGVGIGGTFDKAAKLAKKALLRPIGERN- 215
Query: 181 IIKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPNC 240
P +I L EL +IN LGIG G+GG +T LDVKI YP H AS PVA+ C
Sbjct: 216 -----PDPEIAALEEELLEEINKLGIGPMGLGGKTTALDVKIETYPCHIASLPVAVNIQC 270
Query: 241 AATRHGF 247
A RH
Sbjct: 271 HAARHAE 277
>gnl|CDD|233103 TIGR00722, ttdA_fumA_fumB, hydro-lyases, Fe-S type,
tartrate/fumarate subfamily, alpha region. A number of
Fe-S cluster-containing hydro-lyases share a conserved
motif, including argininosuccinate lyase,
adenylosuccinate lyase, aspartase, class I fumarate
hydratase (fumarase), and tartrate dehydratase (see
PROSITE:PDOC00147). This model represents a subset of
closely related proteins or modules, including the E.
coli tartrate dehydratase alpha chain and the N-terminal
region of the class I fumarase (where the C-terminal
region is homologous to the tartrate dehydratase beta
chain). The activity of archaeal proteins in this
subfamily has not been established.
Length = 273
Score = 201 bits (513), Expect = 2e-60
Identities = 99/250 (39%), Positives = 136/250 (54%), Gaps = 20/250 (8%)
Query: 7 AKDAIAQILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRGY 66
AK + IL N + K P+CQDTG+ F+K+G G +++ I +GV
Sbjct: 36 AKINLEAILDNIEIAEKLGVPVCQDTGVPIFFVKVGSR---FVLIGKLYEAIKQGVEEAT 92
Query: 67 TN-PNNILRASIVSDPHFIRKNTQDNT---PAVINMELVPGNFLDIKIASKGGGSENKTK 122
P LR + V R+NT DNT I++E+VPG+ L+I + KG GSEN +
Sbjct: 93 EEVP---LRPNAVHP--LTRENTGDNTGLGVPQIHVEIVPGDELEIVVFPKGAGSENPSA 147
Query: 123 FAMLNPSDSL---VDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKVLMQDINMN 179
ML PSD + ++++TV G CPP I+G+GIGG+ E A +AKK L++ I
Sbjct: 148 LKMLKPSDGIEGVKKFVLETVKNAGGKPCPPIIVGVGIGGSFETAAKLAKKALLRPIG-- 205
Query: 180 SIIKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPN 239
+ P KI +L LEL +INSLGIG G+GG +T LDVKI H AS PVA+
Sbjct: 206 ---ERHPNPKIAKLELELLEEINSLGIGPMGLGGKTTALDVKIESAHCHTASLPVAVNIQ 262
Query: 240 CAATRHGFLL 249
C A R L+
Sbjct: 263 CWAHRRATLV 272
>gnl|CDD|234650 PRK00122, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 172
Score = 131 bits (332), Expect = 1e-35
Identities = 49/177 (27%), Positives = 85/177 (48%), Gaps = 14/177 (7%)
Query: 402 DHLITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGN 461
+ L+ +G ++ A+GI G + +K F D F + ++I + + H
Sbjct: 5 EDLLVVGKIVSAHGIKGEVKVKSFTDFPERIFDYGPWLL--GKGGEWQEVEIESGRFHKG 62
Query: 462 YVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTV 521
+++ G+ DRN A L+G L + + P+L D +YW +LI V + G+ LG V
Sbjct: 63 FLIVKFEGVDDRNAAEALKGCELFVPRSQLPEL-EEDEYYWHDLIGLEVVDEDGEELGKV 121
Query: 522 TEIIQNKVHSILRIIQSSTKIICTKKYKKKYGILIPFIKIFIKNVDIIKKKIIVDWD 578
T+I++ + +L + KK LIPF++ +K VD+ K+I VDW
Sbjct: 122 TDILETGANDVLVV-----------LKDKKEERLIPFVEEVVKEVDLEAKRITVDWP 167
>gnl|CDD|233805 TIGR02273, 16S_RimM, 16S rRNA processing protein RimM. This family
consists of the bacterial protein RimM (YfjA, 21K), a
30S ribosomal subunit-binding protein implicated in 16S
ribsomal RNA processing. It has been partially
characterized in Escherichia coli, is found with other
translation-associated genes such as trmD. It is broadly
distributed among bacteria, including some minimal
genomes such the aphid endosymbiont Buchnera aphidicola.
The protein contains a PRC-barrel domain that it shares
with other protein families (pfam05239) and a unique
domain (pfam01782). This model describes the full-length
protein. A member from Arabidopsis (plant) has
additional N-terminal sequence likely to represent a
chloroplast transit peptide [Transcription, RNA
processing].
Length = 165
Score = 128 bits (324), Expect = 1e-34
Identities = 50/175 (28%), Positives = 84/175 (48%), Gaps = 12/175 (6%)
Query: 404 LITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNYV 463
L+ +G + +GI G + +K F D F + + ++K+ + N +
Sbjct: 1 LLVVGKIGGPHGIKGEVKVKSFTDFPESLFDYGPWLILKGSK-QWQTVKVARVRKQNNKL 59
Query: 464 LANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVTE 523
+ GI DR A L+G L + P+L D +YW +LI V G+ LG V E
Sbjct: 60 IVKFEGIDDREAAEALKGLELFVPREALPEL-EEDEYYWTDLIGLEVVTEEGEELGKVVE 118
Query: 524 IIQNKVHSILRIIQSSTKIICTKKYKKKYGILIPFIKIFIKNVDIIKKKIIVDWD 578
I++ + +L ++ +KK KK+ +LIPF++ +K +D+ KK I VDW
Sbjct: 119 ILETGANDVL--------VVRSKKGKKE--VLIPFVEEIVKEIDLEKKIITVDWP 163
>gnl|CDD|223877 COG0806, RimM, RimM protein, required for 16S rRNA processing
[Translation, ribosomal structure and biogenesis].
Length = 174
Score = 118 bits (298), Expect = 5e-31
Identities = 53/175 (30%), Positives = 84/175 (48%), Gaps = 12/175 (6%)
Query: 404 LITIGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNYV 463
L+ +G ++ +GI G + +K F D F W + + + + + H N +
Sbjct: 7 LLLVGKIVSTHGIRGEVRVKSFTDFPESLF-DYGPWLLLKPGGEWQELTVESVRKHKNLL 65
Query: 464 LANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVTE 523
+ GI DRN A L+GY + + ++ P+L D FY+ +LI V G+LLG VTE
Sbjct: 66 ILKFKGIDDRNAAEALKGYEIFVDRSELPEL-EEDEFYYHDLIGLEVVTEDGELLGKVTE 124
Query: 524 IIQNKVHSILRIIQSSTKIICTKKYKKKYGILIPFIKIFIKNVDIIKKKIIVDWD 578
I++ + +L + K K LIPF+ +K VD+ KKI VD D
Sbjct: 125 ILETGANDVLVV----------KAKGGKKERLIPFVDAVVKEVDLEAKKIEVDPD 169
>gnl|CDD|237955 PRK15389, PRK15389, fumarate hydratase; Provisional.
Length = 536
Score = 111 bits (279), Expect = 7e-26
Identities = 83/251 (33%), Positives = 116/251 (46%), Gaps = 34/251 (13%)
Query: 13 QILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRGYTNPNNI 72
+L N+ + A P+CQDTG + K G V + G + ++ GV YT N
Sbjct: 88 DLLKNANIAAGGVLPMCQDTGTAIIMGKKGQRV-WTGGDDEEA--LSRGVYDTYTELN-- 142
Query: 73 LRASIVSDPH--FIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKTKF-----AM 125
LR S + P + KNT N PA I++ G+ +KGGGS NKT A+
Sbjct: 143 LRYSQNA-PLDMYEEKNTGTNLPAQIDIYATEGDEYKFLFMAKGGGSANKTFLYQETKAL 201
Query: 126 LNPSDSLVDWIMKTVPTMGAGWCPPGILGIGIGGT-PEKAMLMAKKVLMQDINMNSI--I 182
LNP D L+ ++++ + T+G CPP L I IGGT E + K + S +
Sbjct: 202 LNP-DRLLAFLVEKMRTLGTAACPPYHLAIVIGGTSAEANLKTVK--------LASAKYL 252
Query: 183 KNGPKNKIE--------ELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPV 234
P E EL E+ LGIGAQ GG DV+++ P H AS PV
Sbjct: 253 DALPTEGNEHGHAFRDLELEQEVLKLTQKLGIGAQ-FGGKYFCHDVRVIRLPRHGASCPV 311
Query: 235 AIIPNCAATRH 245
I +C+A R+
Sbjct: 312 GIGVSCSADRN 322
>gnl|CDD|163429 TIGR03717, R_switched_YjbE, integral membrane protein, YjbE family.
Rfam model RF00080 describes a structured RNA element
called the yybP-ykoY leader, or SraF, which may precede
one or several genes in a genome. Members of this highly
hydrophobic protein family commonly are preceded by a
yybP-ykoY leader, which may serve as a riboswitch. From
the larger group of TerC homologs (pfam03741), this
subfamily contains protein YjbE from Bacillus subtilis.
A transport function is proposed.
Length = 176
Score = 102 bits (257), Expect = 2e-25
Identities = 47/106 (44%), Positives = 65/106 (61%), Gaps = 7/106 (6%)
Query: 246 GFLLFWISIKLLSNDHNYTT--IASGKNLIHAIKTIIFADLIMSIDNVLAIAGTASQISN 303
G LL WI KLL + + L AIKTI+ AD +MS+DNVLA+AG A
Sbjct: 68 GLLLLWIGWKLLLEEEEEQGGDVKGSTTLWAAIKTIVIADAVMSLDNVLAVAGAA----- 122
Query: 304 KYQMLLVIIGILFSIPIIIFGSKLVLILIEKFSSIIILCSILLGYL 349
+ L+I G+L SIPII++GS L+L L+++F II + + LLGY+
Sbjct: 123 HGHLGLLIFGLLLSIPIIVWGSTLILKLMDRFPWIIYIGAALLGYV 168
>gnl|CDD|240319 PTZ00226, PTZ00226, fumarate hydratase; Provisional.
Length = 570
Score = 109 bits (275), Expect = 3e-25
Identities = 80/243 (32%), Positives = 116/243 (47%), Gaps = 20/243 (8%)
Query: 13 QILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRGYTNPNNI 72
+L N+ + A P CQDTG V K G + G +++GV YTN N
Sbjct: 118 TLLKNACIAAGRVLPGCQDTGTAIVLGKRGELIWT---GGEDEKALSKGVYNAYTNRN-- 172
Query: 73 LRASIVSD-PHFIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKTKF-----AML 126
LR S ++ F KNT N PA I++ PGN + +KGGGS NKT ++L
Sbjct: 173 LRYSQLAPLDMFDEKNTGCNLPAQIDLYATPGNEYEFLFIAKGGGSANKTFLYQQTKSLL 232
Query: 127 NPSDSLVDWIMKTVPTMGAGWCPPGILGIGIGGT-PEKAMLMAKKVLMQDINMNSIIKNG 185
NP SL ++ + + T+G CPP L + IGG E + K L +S+ +G
Sbjct: 233 NP-KSLRKFLEEKIKTIGTSACPPYHLAVVIGGLSAEMTLKTVK--LASCRYYDSLPTSG 289
Query: 186 PKN----KIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPNCA 241
+ + E + K ++GIGAQ GG DV+++ P H AS P+ I +C+
Sbjct: 290 DEYGRAFRDLEWEEIILEKTQNIGIGAQ-FGGKYFAHDVRVIRLPRHGASCPIGIGVSCS 348
Query: 242 ATR 244
A R
Sbjct: 349 ADR 351
>gnl|CDD|215068 PLN00133, PLN00133, class I-fumerate hydratase; Provisional.
Length = 576
Score = 102 bits (255), Expect = 8e-23
Identities = 80/244 (32%), Positives = 112/244 (45%), Gaps = 22/244 (9%)
Query: 13 QILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRGYTNPNNI 72
++L N+ + A P CQDTG V K G V +G + ++ GV YT+ N
Sbjct: 125 ELLKNANIAAGRVLPGCQDTGTAIVMGKRGQRVLT---DGEDEEHLSRGVYDAYTDTN-- 179
Query: 73 LRASIVSD-PHFIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKTKF-----AML 126
LR S V+ F KNT N PA I++ G+ + +KGGGS NKT A+L
Sbjct: 180 LRYSQVAPLDMFEEKNTGTNLPAQIDLYAAKGDEYHFQFIAKGGGSANKTFLYQQTKALL 239
Query: 127 NPSDSLVDWIMKTVPTMGAGWCPPGILGIGIGGTPE----KAMLMAKKVLMQDINMNSII 182
N SL ++ + + T+G CPP L I IGG K + +A + +
Sbjct: 240 NEG-SLEAFLEEKIKTIGTSACPPYHLAIVIGGLSAEQNLKTVKLASTRYYDTLPTSG-- 296
Query: 183 KNGPKNKIEELRLE--LFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPNC 240
N +L E + LGIGAQ GG DV+++ P H AS PV I +C
Sbjct: 297 -NALGRAFRDLEWEEKILKMTRGLGIGAQ-FGGKYFCHDVRVIRLPRHGASCPVGIGVSC 354
Query: 241 AATR 244
+A R
Sbjct: 355 SADR 358
>gnl|CDD|181309 PRK08230, PRK08230, tartrate dehydratase subunit alpha; Validated.
Length = 299
Score = 97.5 bits (243), Expect = 2e-22
Identities = 72/259 (27%), Positives = 119/259 (45%), Gaps = 30/259 (11%)
Query: 17 NSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRG-YTNPNNILRA 75
N ++ RP CQDTG++ F+K+G G + ++ E V P LR
Sbjct: 55 NQQLAIDLNRPSCQDTGVIQFFVKVGARFPLLG---ELESILKEAVEEATVKAP---LRH 108
Query: 76 SIVSDPHFIRKNTQDNT----PAVINMELVPGN-FLDIKIASKGGGSENKTKFAMLNPS- 129
+ V F NT NT P V E+VP + +I++ GGG + +L P
Sbjct: 109 NAVET--FDEYNTGKNTGSGVPWV-FWEIVPDSDDAEIEVYMAGGGCTLPGRAKVLMPGE 165
Query: 130 --DSLVDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKVLMQDINMNSIIKNGPK 187
+ +V ++ + + G CPP ++G+GI + E A +++KK +++ I + P
Sbjct: 166 GYEGVVKFVFDVITSYGVNACPPLLVGVGIATSVETAAVLSKKAILRPIGSRN-----PN 220
Query: 188 NKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPNCAATRHGF 247
+ EL L +N +G+G QG+ G S+V+ V I H ++ VA+ C A R G
Sbjct: 221 PRAAELEKRLEEGLNRIGLGPQGLTGNSSVMGVNIESAARHPSTIGVAVSTGCWAHRRGT 280
Query: 248 LLFWISIKLLSNDHNYTTI 266
++F D NY +
Sbjct: 281 IVF-------DADLNYEIL 292
>gnl|CDD|185289 PRK15391, PRK15391, fumarate hydratase FumB; Provisional.
Length = 548
Score = 93.2 bits (231), Expect = 5e-20
Identities = 78/247 (31%), Positives = 118/247 (47%), Gaps = 26/247 (10%)
Query: 13 QILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRGYTNPNNI 72
Q L NS + AK P CQDTG + K G V + G G + +++GV Y N
Sbjct: 89 QFLRNSEIAAKGVLPTCQDTGTAIIVGKKGQRV-WTG--GGDEEALSKGVYNTYIEDN-- 143
Query: 73 LRASIVSDPHFIRK-NTQDNTPAVINMELVPGNFLDIKIASKGGGSENKTKF-----AML 126
LR S + ++ NT N PA I++ V G+ +KGGGS NKT A+L
Sbjct: 144 LRYSQNAALDMYKEVNTGTNLPAQIDLYAVDGDEYKFLCVAKGGGSANKTYLYQETKALL 203
Query: 127 NPSDSLVDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKV--------LMQDINM 178
P L +++++ + T+G CPP + IGGT + L K+ L + N
Sbjct: 204 TPG-KLKNFLVEKMRTLGTAACPPYHIAFVIGGTSAETNLKTVKLASAHYYDELPTEGN- 261
Query: 179 NSIIKNGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIP 238
++G + +L EL + LG+GAQ GG D++++ P H AS PV +
Sbjct: 262 ----EHGQAFRDVQLEQELLEEAQKLGLGAQ-FGGKYFAHDIRVIRLPRHGASCPVGMGV 316
Query: 239 NCAATRH 245
+C+A R+
Sbjct: 317 SCSADRN 323
>gnl|CDD|234588 PRK00040, rpsP, 30S ribosomal protein S16; Reviewed.
Length = 75
Score = 81.3 bits (202), Expect = 4e-19
Identities = 28/55 (50%), Positives = 36/55 (65%)
Query: 351 ATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLI 405
DSR+ RDGRFIER+GFYNPLA E++ K+ R YW GA+ + TV L+
Sbjct: 21 VADSRSPRDGRFIERVGFYNPLAKPAEEEVKLDEERVLYWLGQGAQPTDTVRRLL 75
>gnl|CDD|185288 PRK15390, PRK15390, fumarate hydratase FumA; Provisional.
Length = 548
Score = 90.1 bits (223), Expect = 5e-19
Identities = 77/242 (31%), Positives = 114/242 (47%), Gaps = 16/242 (6%)
Query: 13 QILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRGYTNPNNI 72
Q L NS + AK P CQDTG + K G V G + + + GV Y N
Sbjct: 89 QFLRNSDIAAKGVLPTCQDTGTAIIVGKKGQRVWTGGGDEA---ALARGVYNTYIEDN-- 143
Query: 73 LRASIVSDPHFIRK-NTQDNTPAVINMELVPGNFLDIKIASKGGGSENKTKF-----AML 126
LR S + ++ NT N PA I++ V G+ +KGGGS NKT A+L
Sbjct: 144 LRYSQNAPLDMYKEVNTGTNLPAQIDLYAVDGDEYKFLCIAKGGGSANKTYLYQETKALL 203
Query: 127 NPSDSLVDWIMKTVPTMGAGWCPPGILGIGIGGTPEKAMLMAKKVLMQ---DINMNSIIK 183
P L +++++ + T+G CPP + IGGT + L K+ D +
Sbjct: 204 TPG-KLKNYLVEKMRTLGTAACPPYHIAFVIGGTSAETNLKTVKLASAKYYDELPTEGNE 262
Query: 184 NGPKNKIEELRLELFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPNCAAT 243
+G + EL EL + +LG+GAQ GG D++++ P H AS PV + +C+A
Sbjct: 263 HGQAFRDVELEKELLIEAQNLGLGAQ-FGGKYFAHDIRVIRLPRHGASCPVGMGVSCSAD 321
Query: 244 RH 245
R+
Sbjct: 322 RN 323
>gnl|CDD|185290 PRK15392, PRK15392, putative fumarate hydratase; Provisional.
Length = 550
Score = 88.5 bits (219), Expect = 2e-18
Identities = 64/241 (26%), Positives = 114/241 (47%), Gaps = 14/241 (5%)
Query: 13 QILINSRMCAKEKRPICQDTGIVNVFLKIGMNVRFKGFNGSIHDVINEGVRRGYTNPNNI 72
Q+L N+ + AK P CQDTG + G + + G N + + +++G+ + NN+
Sbjct: 88 QLLRNAEVSAKGVLPNCQDTGTATIVASKGQQI-WTGGNDA--EALSKGIYSTFQE-NNL 143
Query: 73 LRASIVSDPHFIRKNTQDNTPAVINMELVPGNFLDIKIASKGGGSENKTKF-----AMLN 127
+ + NTQ N PA I++ V G+ +KGGGS NK ++L
Sbjct: 144 RFSQNAPLDMYTEVNTQTNLPAQIDISAVAGDEYHFLCVNKGGGSANKAALYQETKSLLQ 203
Query: 128 PSDSLVDWIMKTVPTMGAGWCPPGILGIGIGG-TPEKAMLMAKKVLMQDINMNSIIKNGP 186
P + L ++++ + ++G CPP + +GG + ++ + +AK + + N
Sbjct: 204 P-EKLTAFLIEKMKSLGTAACPPYHIAFVVGGLSADQTLKVAKLASTKYYDNLPTSGNEQ 262
Query: 187 KNKIEELRLE--LFNKINSLGIGAQGMGGLSTVLDVKIMMYPTHAASKPVAIIPNCAATR 244
++ LE L GIGAQ GG D++++ P H S P+A+ +C+A R
Sbjct: 263 GQAFRDIELEKVLLEASQQFGIGAQ-FGGKYFAHDIRVIRLPRHGGSCPIAMALSCSADR 321
Query: 245 H 245
+
Sbjct: 322 N 322
>gnl|CDD|216173 pfam00886, Ribosomal_S16, Ribosomal protein S16.
Length = 61
Score = 72.5 bits (179), Expect = 3e-16
Identities = 22/48 (45%), Positives = 30/48 (62%)
Query: 351 ATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTS 398
DSR+ RDGRFIE +G YNP+A +E + K+ R YW GA+ +
Sbjct: 14 VADSRSPRDGRFIEELGTYNPIAKPQEPEVKLDEERIKYWLGKGAQPT 61
>gnl|CDD|217707 pfam03741, TerC, Integral membrane protein TerC family. This
family contains a number of integral membrane proteins
that also contains the TerC protein. TerC has been
implicated in resistance to tellurium. This protein may
be involved in efflux of tellurium ions. The
tellurite-resistant Escherichia coli strain KL53 was
found during testing of the group of clinical isolates
for antibiotics and heavy metal ion resistance.
Determinant of the tellurite resistance of the strain
was located on a large conjugative plasmid. Analyses
showed, the genes terB, terC, terD and terE are
essential for conservation of the resistance. The
members of the family contain a number of conserved
aspartates that could be involved in binding to metal
ions.
Length = 184
Score = 75.6 bits (187), Expect = 7e-16
Identities = 31/118 (26%), Positives = 52/118 (44%), Gaps = 18/118 (15%)
Query: 246 GFLLFWISIKLLSNDHNY------------TTIASGKNLIHAIKTIIFADLIMSIDNVLA 293
G L + +IKLL + + +L A+ I ADL+ S+D+V A
Sbjct: 67 GAFLLYTAIKLLRENEEDDEENKIVRELKKVLPVTSSSLWLAVIQIELADLVFSLDSVPA 126
Query: 294 IAGTASQISNKYQMLLVIIGILFSIPIIIFGSKLVLILIEKFSSIIILCSILLGYLSA 351
G +VI G +F+I + F + L+ LIE+F + L + +LG++
Sbjct: 127 AVGITDDP------FIVITGNIFAILGLRFLAFLLAKLIERFPYLKYLAAAILGFIGV 178
Score = 34.4 bits (80), Expect = 0.074
Identities = 19/77 (24%), Positives = 36/77 (46%), Gaps = 8/77 (10%)
Query: 278 TIIFADLIMSIDNVLAIAGTASQISNKYQMLLVIIGIL----FSIPIIIFGSKLVLILIE 333
T+ ++ +S+DN IA ++ + Q + GI+ I +I+ GS L+E
Sbjct: 2 TLYLLEISLSVDNAFVIALIFRKLPPEQQKKALFWGIIGALVLRIILILLGSA----LLE 57
Query: 334 KFSSIIILCSILLGYLS 350
F I+++ L Y +
Sbjct: 58 LFDWILLIGGAFLLYTA 74
>gnl|CDD|223306 COG0228, RpsP, Ribosomal protein S16 [Translation, ribosomal
structure and biogenesis].
Length = 87
Score = 68.4 bits (168), Expect = 2e-14
Identities = 28/56 (50%), Positives = 35/56 (62%), Gaps = 1/56 (1%)
Query: 351 ATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLIT 406
DSR+ RDGRFIER+G YNPL KE++ K+ R YW GA+ S TV L+
Sbjct: 21 VADSRSPRDGRFIERLGTYNPL-LGKEERVKLDEERILYWLSQGAQPSDTVRRLLK 75
>gnl|CDD|223930 COG0861, TerC, Membrane protein TerC, possibly involved in
tellurium resistance [Inorganic ion transport and
metabolism].
Length = 254
Score = 73.0 bits (180), Expect = 2e-14
Identities = 20/82 (24%), Positives = 41/82 (50%), Gaps = 6/82 (7%)
Query: 267 ASGKNLIHAIKTIIFADLIMSIDNVLAIAGTASQISNKYQMLLVIIGILFSIPIIIFGSK 326
AI I ADL+ S+D+V+A G A +++ ++F+I ++ F +
Sbjct: 128 KKATPFWGAIIQIELADLVFSLDSVIAAVGMAGHP------FVMVTAVIFAILVMRFAAF 181
Query: 327 LVLILIEKFSSIIILCSILLGY 348
L+ L+E+ ++ L ++L +
Sbjct: 182 LLARLLERHPTLKYLALVILLF 203
>gnl|CDD|172989 PRK14523, rpsP, 30S ribosomal protein S16; Provisional.
Length = 137
Score = 67.2 bits (163), Expect = 2e-13
Identities = 26/58 (44%), Positives = 39/58 (67%)
Query: 348 YLSATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLI 405
++ D R RDGRFIER+G+YNP+A ++ + ++ R ++W GA+TSL V HLI
Sbjct: 18 HIVVADRRKPRDGRFIERVGYYNPMARGQDIRLQLEKERISHWLNQGAQTSLRVKHLI 75
>gnl|CDD|216696 pfam01782, RimM, RimM N-terminal domain. The RimM protein is
essential for efficient processing of 16S rRNA. The RimM
protein was shown to have affinity for free ribosomal
30S subunits but not for 30S subunits in the 70S
ribosomes. This N-terminal domain is found associated
with a PRC-barrel domain.
Length = 84
Score = 60.6 bits (148), Expect = 9e-12
Identities = 18/84 (21%), Positives = 37/84 (44%), Gaps = 1/84 (1%)
Query: 407 IGVVLRAYGIFGWILIKLFLDDKNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNYVLAN 466
+G ++ +G+ G + +K F D F WF + + + + + H ++
Sbjct: 2 VGKIVGTHGLKGEVKVKSFTDFPEAIF-DYGPWFLLKKKGEWKPLTVESVRLHKKGLIVK 60
Query: 467 LYGITDRNLATKLQGYYLKISIND 490
G+ DR+ A L+G L + +D
Sbjct: 61 FEGVDDRDAAEALKGAELYVPRSD 84
>gnl|CDD|129114 TIGR00002, S16, ribosomal protein S16. This model describes
ribosomal S16 of bacteria and organelles [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 78
Score = 58.8 bits (143), Expect = 4e-11
Identities = 26/56 (46%), Positives = 36/56 (64%), Gaps = 2/56 (3%)
Query: 351 ATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLIT 406
DSR+ RDGR+IE +GFYNPL KE + K+ + R YW GA+ + TV +L+
Sbjct: 20 VADSRSRRDGRYIEELGFYNPL--TKESRVKLNVERIKYWLSKGAQPTDTVRNLLK 73
>gnl|CDD|172991 PRK14525, rpsP, 30S ribosomal protein S16; Provisional.
Length = 88
Score = 58.5 bits (141), Expect = 8e-11
Identities = 22/55 (40%), Positives = 39/55 (70%), Gaps = 2/55 (3%)
Query: 351 ATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLI 405
ATDSRN+RDG+++E +G Y+P +K+ ++ ++ + R +W + GAK S TV ++
Sbjct: 22 ATDSRNARDGKYLEDVGIYDP--TKRPERIELKVERIEHWLKAGAKPSQTVAMIL 74
>gnl|CDD|173054 PRK14590, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 171
Score = 60.3 bits (146), Expect = 1e-10
Identities = 43/175 (24%), Positives = 76/175 (43%), Gaps = 19/175 (10%)
Query: 405 ITIGVVLRAYGIFGWILIKLFLDDKNIFFYAR----KIWFFDPNSLKLFSIKILNKKNHG 460
I++G + + +GI GW+ ++ + + + K+ DP I +L + HG
Sbjct: 1 ISLGQLGKPFGIKGWL--RVNVRGETLHTLKAPATLKLGKEDPQ-FPESEIALLEIRPHG 57
Query: 461 NYVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLG- 519
L G A K +G L + PK+ + FY +LI + GK L
Sbjct: 58 GKFLVRFEGYDTPEEAVKWRGGSLFLPQELLPKIETKGEFYSEDLIGLQAIDETGKPLNW 117
Query: 520 TVTEIIQNKVHSILRIIQSSTKIICTKKYKKKYGILIPFIKIFIKNVDIIKKKII 574
+T++ N H IL I+ + ILIPF+ +F+ ++D+ K+ I+
Sbjct: 118 KLTDVQDNPAHPILVFIKGEGE-----------EILIPFLNVFVGDLDLEKQTIV 161
>gnl|CDD|173056 PRK14592, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 165
Score = 54.0 bits (130), Expect = 2e-08
Identities = 46/173 (26%), Positives = 80/173 (46%), Gaps = 18/173 (10%)
Query: 404 LITIGVVLRAYGIFGWILIKLFLDD-KNIFFYARKIWFFDPNSLKLFSIKILNKKNHGNY 462
LI +GV+ +GI G + IK F +D +NI Y + N+ K+ + ++ N
Sbjct: 2 LICLGVITSPHGIKGHVKIKTFTEDPENISAYGKLT--DGSNTYKISVVSVIGA----NL 55
Query: 463 VLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVT 522
V+A + GI R A L+ L + + P L+ D FY +LI V+ + G +
Sbjct: 56 VIAKISGINSRTEAELLRNKKLYVERSKLPN-LNEDEFYQSDLIGMEVKLEDNTIYGYIK 114
Query: 523 EIIQNKVHSILRIIQSSTKIICTKKYKKKYGILIPFIKIFIKNVDIIKKKIIV 575
+I I+ I +STK K ++PF K ++++ ++ II+
Sbjct: 115 KIYNFGSCDIIEISLTSTK----KS------TMLPFTKEIFPHINVKERYIIL 157
>gnl|CDD|173055 PRK14591, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 169
Score = 48.9 bits (116), Expect = 9e-07
Identities = 34/112 (30%), Positives = 58/112 (51%), Gaps = 13/112 (11%)
Query: 467 LYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVTEIIQ 526
L I + + A K + + P+L + D Y+ +LI C V+NI+ G V +II+
Sbjct: 68 LANINNADTAKKYVNALIGVPKRALPQL-AEDEVYFKDLIGCSVKNINNDSFGVVVDIIE 126
Query: 527 NKVHSILRIIQSSTKIICTKKYKKKYGILIPFIKIFIKNVDIIKKKIIVDWD 578
+ +L +C K+ +Y LIP++K +I + D+ KKI+VDW+
Sbjct: 127 TGANEVL---------VC-KEDNSEY--LIPYVKQYIVSEDLNSKKIVVDWE 166
>gnl|CDD|184724 PRK14520, rpsP, 30S ribosomal protein S16; Provisional.
Length = 155
Score = 47.0 bits (112), Expect = 3e-06
Identities = 25/56 (44%), Positives = 31/56 (55%), Gaps = 4/56 (7%)
Query: 353 DSRNSRDGRFIERIGFYNPLASKKEKKF-KILLNRFTYWKQVGAKTSLTVDHLITI 407
DSR RDGR IE IG Y+P K+E +I R YW VGA+ + V L+ I
Sbjct: 24 DSRTKRDGRAIEEIGRYHP---KEEPSLIEIDSERAQYWLSVGAQPTEPVLALLKI 76
>gnl|CDD|237744 PRK14521, rpsP, 30S ribosomal protein S16; Provisional.
Length = 186
Score = 47.1 bits (112), Expect = 4e-06
Identities = 26/65 (40%), Positives = 38/65 (58%), Gaps = 7/65 (10%)
Query: 351 ATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLN--RFTYWKQVGAKTSLTVDHLITI- 407
A DSR RDG+FIE+IG YNP + + LN R YW GA+ + T ++++
Sbjct: 22 AADSRAPRDGKFIEKIGTYNPNTNPA----TVDLNFDRAVYWLMNGAQPTDTARNILSYE 77
Query: 408 GVVLR 412
GV+L+
Sbjct: 78 GVLLK 82
>gnl|CDD|172990 PRK14524, rpsP, 30S ribosomal protein S16; Provisional.
Length = 94
Score = 44.5 bits (105), Expect = 6e-06
Identities = 25/65 (38%), Positives = 36/65 (55%), Gaps = 8/65 (12%)
Query: 353 DSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLITIGVVLR 412
DSR RDG +IE +G+YNPL K+ + K+ + R W GA+ S TV + LR
Sbjct: 23 DSRKRRDGAYIESLGYYNPL--KEPYEIKVDVERAVEWILKGAQPSDTVRDI------LR 74
Query: 413 AYGIF 417
+G+
Sbjct: 75 KFGVM 79
>gnl|CDD|176950 CHL00005, rps16, ribosomal protein S16.
Length = 82
Score = 43.9 bits (104), Expect = 9e-06
Identities = 18/67 (26%), Positives = 35/67 (52%), Gaps = 10/67 (14%)
Query: 351 ATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLITIGVV 410
A D R+ R+GR +E++GFY+P+ + + + Y+ + GA+ + TV +
Sbjct: 21 AIDVRSRREGRDLEKVGFYDPIK----NQTYLNVPAILYFLEKGAQPTETVYDI------ 70
Query: 411 LRAYGIF 417
L+ +F
Sbjct: 71 LKKAEVF 77
>gnl|CDD|184351 PRK13828, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 161
Score = 40.7 bits (96), Expect = 5e-04
Identities = 34/155 (21%), Positives = 61/155 (39%), Gaps = 29/155 (18%)
Query: 437 KIWFF--DPNSL------------KLFSIKILNK-KNHGNYVLANLYGITDRNLATKLQG 481
++ F DP ++ + F++ + K+ ++A L G+ R A L+G
Sbjct: 6 RLKSFTEDPLAIADYGPLTTEDGARSFTVALARPAKDG---LVARLKGVATREAAEALRG 62
Query: 482 YYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLLGTVTEIIQNKVHSILRIIQSSTK 541
L + + P+L D FY +LI + G LLG V + IL I
Sbjct: 63 LELYVPRDRLPEL-DDDEFYHADLIGLAAVDTGGALLGRVKAVHNFGAGDILEIAPPG-- 119
Query: 542 IICTKKYKKKYGILIPFIKIFIKNVDIIKKKIIVD 576
+L+PF + + VD+ +++ D
Sbjct: 120 --------GGPTLLLPFTRAVVPTVDLAAGRVVAD 146
>gnl|CDD|218519 pfam05239, PRC, PRC-barrel domain. The PRC-barrel is an all beta
barrel domain found in photosystem reaction centre
subunit H of the purple bacteria and RNA metabolism
proteins of the RimM group. PRC-barrels are
approximately 80 residues long, and found widely
represented in bacteria, archaea and plants. This domain
is also present at the carboxyl terminus of the
pan-bacterial protein RimM, which is involved in
ribosomal maturation and processing of 16S rRNA. A
family of small proteins conserved in all known
euryarchaea are composed entirely of a single
stand-alone copy of the domain.
Length = 78
Score = 38.1 bits (89), Expect = 8e-04
Identities = 25/79 (31%), Positives = 37/79 (46%), Gaps = 8/79 (10%)
Query: 498 DTFYWFNLIDCIVENIHGKLLGTVTEIIQNKVHSILRIIQSSTKIICTKKYKKKYGILIP 557
D FY +LI V G+ LG V +++ ++ +R + S K +LIP
Sbjct: 2 DEFYASDLIGLEVYTEDGEKLGKVKDVVIDEGEGDVRYLVVSVGGFLGSKE-----VLIP 56
Query: 558 FIKIFIKNVDIIKKKIIVD 576
F K NV + K +IIVD
Sbjct: 57 FDK---LNVKLGKDRIIVD 72
>gnl|CDD|172988 PRK14522, rpsP, 30S ribosomal protein S16; Provisional.
Length = 116
Score = 37.3 bits (86), Expect = 0.003
Identities = 21/75 (28%), Positives = 38/75 (50%), Gaps = 7/75 (9%)
Query: 349 LSATDSRNSRDGRFIERIGFYNPLASKKEKKFKILLNRFTYWKQVGAKTSLTVDHLITIG 408
L D + RDG++IE +G+Y+P E+ +++ R YW GA+ + L+ G
Sbjct: 20 LVLADVESPRDGKYIELLGWYDP---HSEQNYQLKSERIFYWLNQGAELTEKAGALVKQG 76
Query: 409 VVLRAYGIFGWILIK 423
A G++ ++ K
Sbjct: 77 ----APGVYSELMAK 87
>gnl|CDD|234326 TIGR03716, R_switched_YkoY, integral membrane protein, YkoY family.
Rfam model RF00080 describes a structured RNA element
called the yybP-ykoY leader, or SraF, which may precede
one or several genes in a genome. Members of this highly
hydrophobic protein family often are preceded by a
yybP-ykoY leader, which may serve as a riboswitch. From
the larger group of TerC homologs (pfam03741), this
subfamily contains proteins YceF and YkoY from Bacillus
subtilis. A transport function is proposed.
Length = 215
Score = 34.2 bits (79), Expect = 0.13
Identities = 16/69 (23%), Positives = 35/69 (50%), Gaps = 6/69 (8%)
Query: 281 FADLIMSIDNVLAIAGTASQISNKYQMLLVIIGILFSIPIIIFGSKLVLILIEKFSSIII 340
D+ S+D++LA + Q +V +G + I I+ F + + + L+E+F +
Sbjct: 104 LMDIAFSVDSILAAVALSGQF------WVVFLGGIIGILIMRFAATIFVKLLERFPELET 157
Query: 341 LCSILLGYL 349
+L+G++
Sbjct: 158 AAFLLIGWI 166
>gnl|CDD|184352 PRK13829, rimM, 16S rRNA-processing protein RimM; Provisional.
Length = 162
Score = 33.6 bits (77), Expect = 0.14
Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 2/66 (3%)
Query: 459 HGNYVLANLYGITDRNLATKLQGYYLKISINDFPKLLSSDTFYWFNLIDCIVENIHGKLL 518
G ++ +L G+T R A L G + D P L ++Y+ L V + G+ L
Sbjct: 49 VGPELVLHLAGVTSREGAEALVGLRVYADDADLPP-LEEGSYYYHELRGLPVY-VDGEPL 106
Query: 519 GTVTEI 524
G V ++
Sbjct: 107 GEVVDV 112
>gnl|CDD|179654 PRK03818, PRK03818, putative transporter; Validated.
Length = 552
Score = 31.8 bits (73), Expect = 1.0
Identities = 19/43 (44%), Positives = 22/43 (51%), Gaps = 5/43 (11%)
Query: 287 SIDNVLAIAGTASQISNKYQMLLVIIGI-----LFSIPIIIFG 324
+ID V + G A Q + QML V IGI L SIP I G
Sbjct: 351 AIDAVANVLGNAQQKLQQVQMLPVFIGIGLGVLLGSIPFFIPG 393
>gnl|CDD|214453 MTH00196, ND2, NADH dehydrogenase subunit 2; Provisional.
Length = 365
Score = 29.6 bits (67), Expect = 4.5
Identities = 27/68 (39%), Positives = 34/68 (50%), Gaps = 5/68 (7%)
Query: 404 LITIGVVLRAYGIFGWILIKLFLDDKNIFFYAR--KIWFFDPNSLKLFSIKILNKKNHGN 461
++ GVV + Y IF L+ +F +Y R KI FF NS L S KIL K+N N
Sbjct: 273 ILLSGVVYQYYLIF---LLAVFCSVIAGVYYVRIVKILFFQANSFLLISTKILKKENKIN 329
Query: 462 YVLANLYG 469
A L G
Sbjct: 330 LRKALLIG 337
>gnl|CDD|215412 PLN02769, PLN02769, Probable galacturonosyltransferase.
Length = 629
Score = 29.7 bits (67), Expect = 4.7
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 8/50 (16%)
Query: 424 LFLDDKNIFFYARKIWFFDPNSLKLFSIKILN-----KKNHGNYVLANLY 468
+ D +N +YA K W FD NS K ++++LN K+ + L L
Sbjct: 364 VLTDAQN--YYAMKHW-FDRNSYKEAAVQVLNIEDLILKDLDKFALKQLS 410
>gnl|CDD|132559 TIGR03520, GldE, gliding motility-associated protein GldE. Members
of this protein family are exclusive to the
Bacteroidetes phylum (previously
Cytophaga-Flavobacteria-Bacteroides). GldC is a protein
linked to a type of rapid surface gliding motility found
in certain Bacteroidetes, such as Flavobacterium
johnsoniae and Cytophaga hutchinsonii. GldE was
discovered because of its adjacency to GldD in F.
johnsonii. Overexpression of GldE partially supresses
the effects of a GldB point mutant suggesting that GldB
and GldE interact. Gliding motility appears closely
linked to chitin utilization in the model species
Flavobacterium johnsoniae. Not all Bacteroidetes with
members of this protein family appear to have all of the
genes associated with gliding motility and in fact some
do not appear to express the gliding phenotype.
Length = 408
Score = 29.2 bits (66), Expect = 5.9
Identities = 23/87 (26%), Positives = 35/87 (40%), Gaps = 7/87 (8%)
Query: 382 ILLNRFTYWKQVGAKTSLTVDHLITIGVVLRAYGIFGWILIKLFLDDKNIFF---YARKI 438
+LL G+ + + LI + +V +FG IL K++ + N+ F A I
Sbjct: 66 VLLFTSLSDNLFGSFNTELLRFLIEVVIVTFLILLFGEILPKVYANRNNLKFAKFMAYPI 125
Query: 439 WFFD----PNSLKLFSIKILNKKNHGN 461
D P SL L +I K G
Sbjct: 126 NILDKVFSPISLPLRAITNFIHKKFGK 152
>gnl|CDD|225183 COG2274, SunT, ABC-type bacteriocin/lantibiotic exporters, contain
an N-terminal double-glycine peptidase domain [Defense
mechanisms].
Length = 709
Score = 28.7 bits (65), Expect = 9.2
Identities = 17/85 (20%), Positives = 35/85 (41%), Gaps = 8/85 (9%)
Query: 273 IHAIKTI-IFADLIMSIDNVLAIAGTAS----QISNKYQMLLVIIGILFSIPIIIFGSKL 327
I +K + DN LA +++ + ++ L S+ I+ FG+ L
Sbjct: 342 IETVKALAAEPRFRSQWDNRLAKQVNIGFKTEKLALILNTIKSLLQQLSSVLILWFGAIL 401
Query: 328 VLILIEKFS-SIIILCSILLGYLSA 351
V L + + ++ ++L GY +
Sbjct: 402 V--LEGELTLGQLVAFNMLAGYFIS 424
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
0.324 0.141 0.419
Gapped
Lambda K H
0.267 0.0736 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 30,103,222
Number of extensions: 3102276
Number of successful extensions: 3373
Number of sequences better than 10.0: 1
Number of HSP's gapped: 3276
Number of HSP's successfully gapped: 150
Length of query: 578
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 476
Effective length of database: 6,413,494
Effective search space: 3052823144
Effective search space used: 3052823144
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 62 (27.6 bits)