Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_013451110.1 CALNI_RS04930 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683
(865 letters)
>NCBI__GCF_000183405.1:WP_013451110.1
Length = 850
Score = 1058 bits (2736), Expect = 0.0
Identities = 536/854 (62%), Positives = 658/854 (77%), Gaps = 15/854 (1%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
+ ++Y KHV ER A GI P PL A + + L+NP G+EEFLL LL +RV PGVD A
Sbjct: 4 IFDQYLKHVEERKAMGIPPLPLSPEMTAEVCKALENPEKGKEEFLLSLLRDRVSPGVDPA 63
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
A VKA +LA + +GE KSPL++ E AI +LGTM GGYN+ PL++AL D LA AA AL
Sbjct: 64 AEVKANWLAKVVRGEVKSPLVSKEDAIFMLGTMIGGYNVAPLVEALKDPSLAKSAANALK 123
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
+ +L++ F +V E +K N+YAK+V++SWA+ EWF ++P L +++ + V+KV GE NTD
Sbjct: 124 NVILVYGAFDEVAELSKT-NQYAKEVIESWANGEWFTSKPDLPKEIKLKVYKVDGEINTD 182
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
D SPA A+SRPDIPLHALAM + G I++I + +G+ +A+VGDVV
Sbjct: 183 DFSPAKHAFSRPDIPLHALAM----------GETRFPGGIQEIANFRAEGYQVAFVGDVV 232
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSA NS++W +G+DIP VPNKR GG+ +GG IAPIFFNT +D+G LPI DV+
Sbjct: 233 GTGSSRKSACNSLMWHIGEDIPFVPNKRRGGIVIGGLIAPIFFNTTQDSGGLPIMCDVTG 292
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
+ GDVI + K E+R E GE+L FELK + DE RAGGR+ LIIGR LT KAR
Sbjct: 293 MKTGDVIIIDTVKMEIRK-ENGEVLTKFELKPATIRDEFRAGGRLNLIIGRALTNKARAF 351
Query: 361 LGLPHSDVFRQAKD-VAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGP 419
LGL SD+F +A++ V + +G++LAQK+VG+ACG+ G+ PG CEPKMT+VGSQDTTGP
Sbjct: 352 LGLGESDLFVKAQNPVPKPGQGYTLAQKIVGKACGLPGVLPGTACEPKMTTVGSQDTTGP 411
Query: 420 MTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVI 479
MT DELK+LACL F ADL MQSFCHTAAYPKP DV H TLP F++ RGGVSL+PGDGVI
Sbjct: 412 MTADELKELACLRFQADLFMQSFCHTAAYPKPADVKMHKTLPSFVIARGGVSLKPGDGVI 471
Query: 480 HSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGK 539
HSWLNR+LLPDTVGTGGDSHTRFPIGISFPAGSGLVAFA A G MPLDMPESVLV+FKGK
Sbjct: 472 HSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAGALGFMPLDMPESVLVKFKGK 531
Query: 540 MQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDAS 599
+ PGITLRD+V+AIP AIKQGLLTV KKGKKNIF+GRILE+EGLPDL VEQAFELTDA+
Sbjct: 532 LNPGITLRDVVNAIPYVAIKQGLLTVAKKGKKNIFNGRILEMEGLPDLTVEQAFELTDAA 591
Query: 600 AERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLE 659
AERSAA TIKL++ + ++L SNI L+K MIAEGY D TL+RRI EKWL PELL
Sbjct: 592 AERSAAAATIKLSENSVADFLKSNIALMKEMIAEGYQDAETLKRRIAACEKWLEKPELLS 651
Query: 660 ADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRA 719
D +AEYAAVI+IDL++IKEPIL PNDPDD + LS V G+KIDEVFIGSCMTNIGHFRA
Sbjct: 652 RDENAEYAAVIEIDLSEIKEPILACPNDPDDVKLLSEVAGDKIDEVFIGSCMTNIGHFRA 711
Query: 720 AGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARV 779
AGK+ + K + PTR+W+ PPT+MDAAQL EGYYS++ GAR EIPGCSLCMGNQARV
Sbjct: 712 AGKIWEKEK-EAPTRIWLTPPTKMDAAQLMREGYYSIYSNIGARTEIPGCSLCMGNQARV 770
Query: 780 ADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYV-AQVDKTAV 838
+TV+STSTRNF +R+G GA V+L SAELAA+AAL+GKLPTPE+Y Y+ +V+
Sbjct: 771 RSKSTVISTSTRNFDDRMGDGARVYLGSAELAAIAALLGKLPTPEDYFKYMNERVEPKKT 830
Query: 839 DTYRYLNFNQLSQY 852
+ Y+YL F+++ +
Sbjct: 831 EIYKYLEFHKMGNF 844
Lambda K H
0.317 0.136 0.400
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: 1862
Number of extensions: 66
Number of successful extensions: 6
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: 865
Length of database: 850
Length adjustment: 42
Effective length of query: 823
Effective length of database: 808
Effective search space: 664984
Effective search space used: 664984
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 (21.7 bits)
S2: 56 (26.2 bits)
Align candidate WP_013451110.1 CALNI_RS04930 (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.3613599.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 1435.9 0.0 0 1435.7 0.0 1.0 1 NCBI__GCF_000183405.1:WP_013451110.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000183405.1:WP_013451110.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1435.7 0.0 0 0 2 843 .. 5 845 .. 4 846 .. 0.99
Alignments for each domain:
== domain 1 score: 1435.7 bits; conditional E-value: 0
TIGR00117 2 leeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakg 74
+++y khv er+a gi+plpl + +a++++ l+n+ +++eefll+ll+drv+pgvd aa vka++la++ +g
NCBI__GCF_000183405.1:WP_013451110.1 5 FDQYLKHVEERKAMGIPPLPLSPEMTAEVCKALENPEKGKEEFLLSLLRDRVSPGVDPAAEVKANWLAKVVRG 77
689********************************************************************** PP
TIGR00117 75 evksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelsktneyakqv 147
evkspl+s e+a+ +lgtm+ggynv pl+eal+ d +ak aa+al++ +lv++afd+v+elsktn+yak+v
NCBI__GCF_000183405.1:WP_013451110.1 78 EVKSPLVSKEDAIFMLGTMIGGYNVAPLVEALK--DPSLAKSAANALKNVILVYGAFDEVAELSKTNQYAKEV 148
********************************9..************************************** PP
TIGR00117 148 leswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieqrikalkqk 220
+eswa++ewf k++l+++i+ v+kvdge ntdd+spa +af+rpdiplhalam +++ ++ q+i++++
NCBI__GCF_000183405.1:WP_013451110.1 149 IESWANGEWFTSKPDLPKEIKLKVYKVDGEINTDDFSPAKHAFSRPDIPLHALAMGETRFPGGIQEIANFRAE 221
************************************************************************* PP
TIGR00117 221 gvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdln 293
g+ va+vgdvvgtgssrksa ns++w++g+dipfvpnkr gg+v+gg iapiffnt++dsg lpi +dv ++
NCBI__GCF_000183405.1:WP_013451110.1 222 GYQVAFVGDVVGTGSSRKSACNSLMWHIGEDIPFVPNKRRGGIVIGGLIAPIFFNTTQDSGGLPIMCDVTGMK 294
************************************************************************* PP
TIGR00117 294 egdvikiypykgeitnketevvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapa 366
+gdvi i k ei+++++ev++ f+lkp t+ de raggr+ liigr+lt+kar +lgl+es++f+ka++p
NCBI__GCF_000183405.1:WP_013451110.1 295 TGDVIIIDTVKMEIRKENGEVLTKFELKPATIRDEFRAGGRLNLIIGRALTNKARAFLGLGESDLFVKAQNPV 367
*********************************************************************9986 PP
TIGR00117 367 .esakgftlaqklvgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaay 438
+ ++g+tlaqk+vgkacg+ g++pgt cepk+ttvgsqdttg+mt delkela+l+f+adl +qsfchtaay
NCBI__GCF_000183405.1:WP_013451110.1 368 pKPGQGYTLAQKIVGKACGLPGVLPGTACEPKMTTVGSQDTTGPMTADELKELACLRFQADLFMQSFCHTAAY 440
2679********************************************************************* PP
TIGR00117 439 pkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaat 511
pkp+dvk+hktlp f+ rggv+l+pgdgvihswlnr+llpdtvgtggdshtrfp+gisfpagsglvafa a+
NCBI__GCF_000183405.1:WP_013451110.1 441 PKPADVKMHKTLPSFVIARGGVSLKPGDGVIHSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAGAL 513
************************************************************************* PP
TIGR00117 512 gvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafe 584
g mpldmpesvlv+fkg+l+pgitlrd+vnaipy+aik+glltv kkgk+n+fngrile+eglpdl veqafe
NCBI__GCF_000183405.1:WP_013451110.1 514 GFMPLDMPESVLVKFKGKLNPGITLRDVVNAIPYVAIKQGLLTVAKKGKKNIFNGRILEMEGLPDLTVEQAFE 586
************************************************************************* PP
TIGR00117 585 ltdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeya 657
ltda+aersaa++tikl++++v+++lksni l+kemiaegy+d++tlkrri+a ekwl+ pell+ d +aeya
NCBI__GCF_000183405.1:WP_013451110.1 587 LTDAAAERSAAAATIKLSENSVADFLKSNIALMKEMIAEGYQDAETLKRRIAACEKWLEKPELLSRDENAEYA 659
************************************************************************* PP
TIGR00117 658 avieidlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraagkileaaktvkarlwvvppt 730
avieidl+eikepila+pndpddvkllsevagd+idevfigscmtnighfraagki e++k+ ++r+w++ppt
NCBI__GCF_000183405.1:WP_013451110.1 660 AVIEIDLSEIKEPILACPNDPDDVKLLSEVAGDKIDEVFIGSCMTNIGHFRAAGKIWEKEKEAPTRIWLTPPT 732
************************************************************************* PP
TIGR00117 731 rmdeqqlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaava 803
+md++ql+ egyy+i+++ garte+pgcslcmgnqarv+ ++tv+ststrnfd+r+g ga+vylgsaelaa+a
NCBI__GCF_000183405.1:WP_013451110.1 733 KMDAAQLMREGYYSIYSNIGARTEIPGCSLCMGNQARVRSKSTVISTSTRNFDDRMGDGARVYLGSAELAAIA 805
************************************************************************* PP
TIGR00117 804 allgkiptkeeylalvsekvesakdklyrylnfnelenfe 843
allgk+pt+e+y +++ e+ve++k ++y+yl+f ++ nf+
NCBI__GCF_000183405.1:WP_013451110.1 806 ALLGKLPTPEDYFKYMNERVEPKKTEIYKYLEFHKMGNFK 845
**************************************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (850 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 36.27
//
[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