Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_011372670.1 SUDEN_RS05460 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::A0A2X5AHR8
(852 letters)
>NCBI__GCF_000012965.1:WP_011372670.1
Length = 848
Score = 1108 bits (2867), Expect = 0.0
Identities = 542/850 (63%), Positives = 676/850 (79%), Gaps = 5/850 (0%)
Query: 4 FLEDYKKSVSERKSEGIPPLPLNAKQVEAVVEILTKDPTNAAFAKELLIHRVSPGVDEGA 63
F+EDYK ++ER++ G+PPLPLNA+Q A+VE++ + A +LL +RVSPGVD+ A
Sbjct: 3 FIEDYKAHIAERETLGVPPLPLNAEQTVALVEMIKDKVGDMAQNVDLLTNRVSPGVDDAA 62
Query: 64 KVKAEFLAKLSQKKLECAHISALEATTLLGTMLGGYNVEPLIMGLESQDKNIAKESAKAL 123
VKA FL ++ +K+ IS A ++G MLGGYNV+P++ L S+ + + +AL
Sbjct: 63 YVKAAFLNDIASEKISIPAISPARAVEMMGMMLGGYNVKPMVDALTSKSSEVVDAAKEAL 122
Query: 124 KTTLLVYGSFDKIAAMSKT-NALAKEVLESWANAEWFLNKEPLNECIEACVFKIDGETNT 182
K TLLVY +F+ + + K N A EV++SWA+AEWF ++ L E + VFK+ GETNT
Sbjct: 123 KHTLLVYDAFNDVEELYKAGNTHAAEVIKSWADAEWFTSRPALAEKMTLSVFKVAGETNT 182
Query: 183 DDLSPASDAFTRSDIPLHAKAMLKNRIENYEQRIKAIKTKGVPVAYVGDVVGTGSSRKSA 242
DDLSPAS+AFTRSDIPLHA +ML +++N + IK +K KG P+AYVGDVVGTGSSRKS
Sbjct: 183 DDLSPASEAFTRSDIPLHANSMLVAKMDNPIETIKKLKEKGNPIAYVGDVVGTGSSRKSG 242
Query: 243 TNSIMWHFGKDIPFVPNKRSGGIVIGGVIAPIFFATCEDSGALPIVADVKDLKEGDMIKI 302
NS+ WH G+DIP VPNKR+GG+V+G +IAPIFFATCEDSGALP+ DV +++ GD+I I
Sbjct: 243 VNSVQWHMGEDIPGVPNKRTGGVVLGSIIAPIFFATCEDSGALPLELDVSEMETGDVITI 302
Query: 303 YPYKGEITLNDKVVSSFKLEPETLLDEVRASGRIPLIIGRGLTNKARKFLGLGESEAFKK 362
YPYKGE + K +++FKL P T+ DEVRA GRIPLIIGRGLT+KAR LGLG S+ F
Sbjct: 303 YPYKGEAHKDGKCIATFKLNPNTITDEVRAGGRIPLIIGRGLTSKARGVLGLGASDKFLT 362
Query: 363 PSAPKSDAKGYTLAQKIVGHACGVKGILPGTYCEPKVTTVGSQDTTGAMTRDEVKELASL 422
P KGYTLAQK+VG ACG+ G+ PG Y EP+ +TVGSQDTTG MTRDE+ ELA+L
Sbjct: 363 AEQPADSGKGYTLAQKMVGRACGMSGVRPGMYVEPETSTVGSQDTTGPMTRDEIVELAAL 422
Query: 423 KFDAPFVLQSFCHTAAYPKPSDVSLHATLPGFITQRGGVALHPGDGVIHTWLNRMGLPDT 482
F A V+QSFCHTAAYPKPSD+ +H TLP FI++R GVAL PGDGVIH+WLNRM LPDT
Sbjct: 423 GFSADLVMQSFCHTAAYPKPSDIVMHHTLPDFISKRSGVALRPGDGVIHSWLNRMVLPDT 482
Query: 483 LGTGGDSHTRFPLGISFPAGSGLVAFAAVTGTMPLNMPESVLVRFKGEMNPGITLRDLVN 542
+GTG DSHTRFP+GISFP GSG+VAFA VTG+MPL MPESVLVRFKGE+ PGITLRDLVN
Sbjct: 483 VGTGADSHTRFPIGISFPGGSGIVAFAGVTGSMPLTMPESVLVRFKGELQPGITLRDLVN 542
Query: 543 AIPYYAIKKGLLTVEKKGKINVFNGRILEIEGLPDIKMEQAFELSDASAERSAAACVVRL 602
AIP+ AIK+GLLTVEKKGK N+F GRI+EIEG+PD+K EQAFELSDASAERSAAAC V L
Sbjct: 543 AIPHQAIKEGLLTVEKKGKKNIFAGRIMEIEGMPDMKCEQAFELSDASAERSAAACTVLL 602
Query: 603 NKEPMIEYLKSNIKLIDEMIASGYEDKETLKKRKDAMQAWVDNPVLLEPDSNAQYAAVIE 662
N+EP+IEYLKSN+ L++ MI +GYEDK T+K+R D M+ W+ +P L++PD++A+YAAVIE
Sbjct: 603 NEEPVIEYLKSNVTLLESMIEAGYEDKRTIKRRIDKMKEWLASPSLMKPDADAEYAAVIE 662
Query: 663 IDVAEITEPILACPNDPDDVATLSEVLADTTGKRPHSIDEVFIGSCMTNIGHFRAFGEIV 722
ID+ ITEPILACPNDPDDVATLSEVLA + RP IDEVF+GSCMTNIGH+RA GE++
Sbjct: 663 IDLNTITEPILACPNDPDDVATLSEVLASS---RPTKIDEVFVGSCMTNIGHYRALGEVL 719
Query: 723 KNAPPSQARLWVVPPSKMDEQELINEGYYAIFGAAGARTEVPGCSLCMGNQARVRDNAVV 782
K LWV PP+KMDE++L +GYY FG AGARTE+PGCSLCMGNQARV D+AVV
Sbjct: 720 KGEGKVPTTLWVCPPTKMDEKQLTEDGYYVTFGEAGARTEIPGCSLCMGNQARVADDAVV 779
Query: 783 FSTSTRNFDNRMGRGAKVYLGSAELGAACALLGRIPTKEEYLNLVSEKLESQKDKIYRYM 842
FSTSTRNFDNR+G+GA+VYLGSAEL A C++LGRIPTK EYL ++K+ ++ +IY+Y+
Sbjct: 780 FSTSTRNFDNRLGKGAQVYLGSAELAAVCSILGRIPTKAEYLE-KTKKIIGKESEIYKYL 838
Query: 843 NFNLMENFRL 852
NFNL+++++L
Sbjct: 839 NFNLIKDYKL 848
Lambda K H
0.316 0.134 0.388
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1906
Number of extensions: 77
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 852
Length of database: 848
Length adjustment: 42
Effective length of query: 810
Effective length of database: 806
Effective search space: 652860
Effective search space used: 652860
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (26.2 bits)
Align candidate WP_011372670.1 SUDEN_RS05460 (bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase)
to HMM TIGR00117 (acnB: aconitate hydratase 2 (EC 4.2.1.3))
# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file: ../tmp/path.carbon/TIGR00117.hmm
# target sequence database: /tmp/gapView.2678095.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR00117 [M=844]
Accession: TIGR00117
Description: acnB: aconitate hydratase 2
Scores for complete sequences (score includes all domains):
--- full sequence --- --- best 1 domain --- -#dom-
E-value score bias E-value score bias exp N Sequence Description
------- ------ ----- ------- ------ ----- ---- -- -------- -----------
0 1459.1 0.6 0 1458.9 0.6 1.0 1 NCBI__GCF_000012965.1:WP_011372670.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000012965.1:WP_011372670.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1458.9 0.6 0 0 1 843 [. 3 847 .. 3 848 .] 0.99
Alignments for each domain:
== domain 1 score: 1458.9 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiak 73
++e+y+ h+aer+++g++plplna+q+ alve++k++ ++ ++ ++ll++rv+pgvd+aayvka fl ia
NCBI__GCF_000012965.1:WP_011372670.1 3 FIEDYKAHIAERETLGVPPLPLNAEQTVALVEMIKDKV-GDMAQNVDLLTNRVSPGVDDAAYVKAAFLNDIAS 74
589******************************98765.5699999*************************** PP
TIGR00117 74 gevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyak 145
+++ p is+ +ave++g mlggynv+p+++al sk +++ +aa +al++tllv+daf+dveel k+ n++a
NCBI__GCF_000012965.1:WP_011372670.1 75 EKISIPAISPARAVEMMGMMLGGYNVKPMVDALTSKSSEVVDAAKEALKHTLLVYDAFNDVEELYKAgNTHAA 147
******************************************************************99***** PP
TIGR00117 146 qvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieqrikalk 218
+v++swa+aewf +++laek+t +vfkv getntddlspa++aftr+diplha +ml +k+++ ++ik+lk
NCBI__GCF_000012965.1:WP_011372670.1 148 EVIKSWADAEWFTSRPALAEKMTLSVFKVAGETNTDDLSPASEAFTRSDIPLHANSMLVAKMDNPIETIKKLK 220
************************************************************************* PP
TIGR00117 219 qkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkd 291
+kg p+ayvgdvvgtgssrks +nsv w++g+dip vpnkr+gg+vlg iapiff+t+edsgalp+e dv++
NCBI__GCF_000012965.1:WP_011372670.1 221 EKGNPIAYVGDVVGTGSSRKSGVNSVQWHMGEDIPGVPNKRTGGVVLGSIIAPIFFATCEDSGALPLELDVSE 293
************************************************************************* PP
TIGR00117 292 lnegdvikiypykgeitnketevvatfklkpetlldevraggripliigrgltdkarealglsesevfkkaka 364
+++gdvi+iypykge + k+++ +atfkl+p+t+ devraggripliigrglt+kar +lgl+ s+ f a++
NCBI__GCF_000012965.1:WP_011372670.1 294 METGDVITIYPYKGEAH-KDGKCIATFKLNPNTITDEVRAGGRIPLIIGRGLTSKARGVLGLGASDKFLTAEQ 365
***************75.678**************************************************** PP
TIGR00117 365 paesakgftlaqklvgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaa 437
pa+s+kg+tlaqk+vg+acg+ g+rpg y ep +tvgsqdttg+mtrde+ ela+lgf+adlv+qsfchtaa
NCBI__GCF_000012965.1:WP_011372670.1 366 PADSGKGYTLAQKMVGRACGMSGVRPGMYVEPETSTVGSQDTTGPMTRDEIVELAALGFSADLVMQSFCHTAA 438
************************************************************************* PP
TIGR00117 438 ypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaa 510
ypkp+d+ +h+tlpdfis+r gvalrpgdgvihswlnrm+lpdtvgtg dshtrfp+gisfp gsg+vafa +
NCBI__GCF_000012965.1:WP_011372670.1 439 YPKPSDIVMHHTLPDFISKRSGVALRPGDGVIHSWLNRMVLPDTVGTGADSHTRFPIGISFPGGSGIVAFAGV 511
************************************************************************* PP
TIGR00117 511 tgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqaf 583
tg mpl mpesvlvrfkgelqpgitlrdlvnaip+ aik+glltvekkgk+n+f+gri+eieg+pd+k eqaf
NCBI__GCF_000012965.1:WP_011372670.1 512 TGSMPLTMPESVLVRFKGELQPGITLRDLVNAIPHQAIKEGLLTVEKKGKKNIFAGRIMEIEGMPDMKCEQAF 584
************************************************************************* PP
TIGR00117 584 eltdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaey 656
el+dasaersaa+ct+ ln+epvieylksn+ ll+ mi gyedkrt+krrid+m++wla p+l+++dadaey
NCBI__GCF_000012965.1:WP_011372670.1 585 ELSDASAERSAAACTVLLNEEPVIEYLKSNVTLLESMIEAGYEDKRTIKRRIDKMKEWLASPSLMKPDADAEY 657
************************************************************************* PP
TIGR00117 657 aavieidlaeikepilaapndpddvkllsevagd....aidevfigscmtnighfraagkileaaktvkarlw 725
aavieidl+ i+epila+pndpddv++lsev++ +idevf+gscmtnigh+ra g++l+++++v++ lw
NCBI__GCF_000012965.1:WP_011372670.1 658 AAVIEIDLNTITEPILACPNDPDDVATLSEVLASsrptKIDEVFVGSCMTNIGHYRALGEVLKGEGKVPTTLW 730
********************************999999*********************************** PP
TIGR00117 726 vvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsae 798
v+ppt+mde+ql+e+gyy fg+agarte+pgcslcmgnqarv+d+a+vfststrnfdnrlgkga+vylgsae
NCBI__GCF_000012965.1:WP_011372670.1 731 VCPPTKMDEKQLTEDGYYVTFGEAGARTEIPGCSLCMGNQARVADDAVVFSTSTRNFDNRLGKGAQVYLGSAE 803
************************************************************************* PP
TIGR00117 799 laavaallgkiptkeeylalvsekvesakdklyrylnfnelenfe 843
laav+++lg+iptk eyl+ +k+ ++ ++y+ylnfn +++++
NCBI__GCF_000012965.1:WP_011372670.1 804 LAAVCSILGRIPTKAEYLEKT-KKIIGKESEIYKYLNFNLIKDYK 847
******************986.566677788***********997 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (848 residues searched)
Passed MSV filter: 1 (1); expected 0.0 (0.02)
Passed bias filter: 1 (1); expected 0.0 (0.02)
Passed Vit filter: 1 (1); expected 0.0 (0.001)
Passed Fwd filter: 1 (1); expected 0.0 (1e-05)
Initial search space (Z): 1 [actual number of targets]
Domain search space (domZ): 1 [number of targets reported over threshold]
# CPU time: 0.01u 0.02s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 27.32
//
[ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory