Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_012469942.1 GLOV_RS09360 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683
(865 letters)
>NCBI__GCF_000020385.1:WP_012469942.1
Length = 843
Score = 1022 bits (2642), Expect = 0.0
Identities = 532/854 (62%), Positives = 632/854 (74%), Gaps = 14/854 (1%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
M+E Y H AERAA+GI PL Q L +LL+ PPAG+E FLL+LL RV PGVD A
Sbjct: 1 MIEAYLAHEAERAAQGIPALPLSPEQTTELCKLLEAPPAGKEAFLLNLLKERVSPGVDPA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
A VKA FLA I G KSPL++ A+ +LGTM GGYN+ PL++AL DA+LA AA ALS
Sbjct: 61 AKVKAEFLAGILNGSKKSPLVSKVDAVRILGTMMGGYNVGPLVEALKDAELADEAACALS 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
L++D F D + N AK+V+ SWA+AEWF N+P + E + V VFKV GE NTD
Sbjct: 121 GMTLVYDGF-DQVVALSSSNAAAKKVLTSWANAEWFTNKPGVPETIKVKVFKVEGEINTD 179
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
D SPA DAWSRPDIPLHALAM K P++ +K I + G +A+VGDVV
Sbjct: 180 DFSPAGDAWSRPDIPLHALAMGKTRF----PNR------LKDIADWRAAGNQVAFVGDVV 229
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSA NSVLW MG DIP VPNK+ G+ +GG IAPIFFNT +D+GALPI+ DV+
Sbjct: 230 GTGSSRKSACNSVLWHMGQDIPCVPNKKTAGVIIGGVIAPIFFNTAQDSGALPIKADVTK 289
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
+N GDVI + KGE+ N E GE+++TF+L + + DE RAGGRIPLIIGR +T KAR+A
Sbjct: 290 MNDGDVITINTAKGEITN-EAGEVISTFKLAPNTIADEFRAGGRIPLIIGRAVTEKARKA 348
Query: 361 LGLPHSDVFR-QAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGP 419
LG+ +DVF V ++D+G+SLAQKMVG+ACGV GI PG CEPKMT+VGSQDTTGP
Sbjct: 349 LGMGETDVFTLPVNPVPKADQGYSLAQKMVGKACGVAGILPGTACEPKMTTVGSQDTTGP 408
Query: 420 MTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVI 479
MT DELK+LACL F + + MQSFCHTAAYPKP DV H TLP FI RGGV+L+PGDGVI
Sbjct: 409 MTADELKELACLKFLSPMFMQSFCHTAAYPKPADVKMHKTLPAFIAERGGVALKPGDGVI 468
Query: 480 HSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGK 539
HSWLNR+LLPDTVGTGGDSHTRFPIGISFPAGSGLVAFA A G MPLDMPESVLVRFKG
Sbjct: 469 HSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAGAMGFMPLDMPESVLVRFKGT 528
Query: 540 MQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDAS 599
PGITLRD V+AIP +AIKQGLLTV KK K NIF+GRILE+EGLP+L VEQ FELTDA+
Sbjct: 529 FNPGITLRDAVNAIPYWAIKQGLLTVPKKNKVNIFNGRILEMEGLPELTVEQGFELTDAA 588
Query: 600 AERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLE 659
AERSAA I+L+KE + YL SN+ L+K MIA+GY D +TL+ RI + +WL NP+LLE
Sbjct: 589 AERSAAAGCIQLSKESVATYLRSNVALMKKMIADGYQDPQTLQNRIDAVNEWLKNPQLLE 648
Query: 660 ADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRA 719
AD +AEYAAVI+IDLA+I EPIL PNDPDD + LS V G I +VFIGSCMTNIGHFRA
Sbjct: 649 ADKNAEYAAVIEIDLAEITEPILACPNDPDDVKLLSEVAGTPIQDVFIGSCMTNIGHFRA 708
Query: 720 AGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARV 779
A ++ K R W+ PPTRMD+ L +E +S++ GARIEI GCSLCMGNQARV
Sbjct: 709 AAEIWKGEKFNPNVRTWITPPTRMDSDLLKDEAVFSIYSAFGARIEIAGCSLCMGNQARV 768
Query: 780 ADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEY-QTYVAQVDKTAV 838
DG + STSTRNF +R+G GA VFL SAEL AVAA +GKLPTP E+ Y +V
Sbjct: 769 PDGVNMFSTSTRNFDDRIGNGAKVFLGSAELGAVAAKMGKLPTPAEFLAIYNEKVAPNKE 828
Query: 839 DTYRYLNFNQLSQY 852
YRYL F+++ Y
Sbjct: 829 KIYRYLQFDEMEGY 842
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: 1890
Number of extensions: 76
Number of successful extensions: 5
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: 843
Length adjustment: 42
Effective length of query: 823
Effective length of database: 801
Effective search space: 659223
Effective search space used: 659223
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_012469942.1 GLOV_RS09360 (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.2929580.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 1397.3 0.3 0 1397.1 0.3 1.0 1 NCBI__GCF_000020385.1:WP_012469942.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000020385.1:WP_012469942.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1397.1 0.3 0 0 1 843 [. 1 843 [] 1 843 [] 0.99
Alignments for each domain:
== domain 1 score: 1397.1 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiak 73
++e+y h aeraa+gi+ lpl +q+++l++ll+ +p+++e+fll+ll++rv+pgvd aa+vka+fla i +
NCBI__GCF_000020385.1:WP_012469942.1 1 MIEAYLAHEAERAAQGIPALPLSPEQTTELCKLLEAPPAGKEAFLLNLLKERVSPGVDPAAKVKAEFLAGILN 73
6899********************************************************************* PP
TIGR00117 74 gevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelsktneyakq 146
g kspl+s +av +lgtm+ggynv pl+eal+ d+++a++aa als lv+d fd+v +ls +n+ ak+
NCBI__GCF_000020385.1:WP_012469942.1 74 GSKKSPLVSKVDAVRILGTMMGGYNVGPLVEALK--DAELADEAACALSGMTLVYDGFDQVVALSSSNAAAKK 144
*********************************9..************************************* PP
TIGR00117 147 vleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieqrikalkq 219
vl swa+aewf nk+ ++e+i+v vfkv+ge ntdd+spa da++rpdiplhalam k++ ++ ++ i++ +
NCBI__GCF_000020385.1:WP_012469942.1 145 VLTSWANAEWFTNKPGVPETIKVKVFKVEGEINTDDFSPAGDAWSRPDIPLHALAMGKTRFPNRLKDIADWRA 217
************************************************************************* PP
TIGR00117 220 kgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdl 292
g va+vgdvvgtgssrksa nsvlw++g+dip vpnk++ g+++gg+iapiffnta+dsgalpi++dv ++
NCBI__GCF_000020385.1:WP_012469942.1 218 AGNQVAFVGDVVGTGSSRKSACNSVLWHMGQDIPCVPNKKTAGVIIGGVIAPIFFNTAQDSGALPIKADVTKM 290
************************************************************************* PP
TIGR00117 293 negdvikiypykgeitnketevvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakap 365
n gdvi+i kgeitn+++ev++tfkl p+t+ de raggripliigr++t+kar+alg++e++vf + +p
NCBI__GCF_000020385.1:WP_012469942.1 291 NDGDVITINTAKGEITNEAGEVISTFKLAPNTIADEFRAGGRIPLIIGRAVTEKARKALGMGETDVFTLPVNP 363
**********************************************************************987 PP
TIGR00117 366 a.esakgftlaqklvgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaa 437
++++g++laqk+vgkacgv gi+pgt cepk+ttvgsqdttg+mt delkela+l+f +++ +qsfchtaa
NCBI__GCF_000020385.1:WP_012469942.1 364 VpKADQGYSLAQKMVGKACGVAGILPGTACEPKMTTVGSQDTTGPMTADELKELACLKFLSPMFMQSFCHTAA 436
62789******************************************************************** PP
TIGR00117 438 ypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaa 510
ypkp+dvk+hktlp fi++rggval+pgdgvihswlnr+llpdtvgtggdshtrfp+gisfpagsglvafa a
NCBI__GCF_000020385.1:WP_012469942.1 437 YPKPADVKMHKTLPAFIAERGGVALKPGDGVIHSWLNRLLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAGA 509
************************************************************************* PP
TIGR00117 511 tgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqaf 583
+g mpldmpesvlvrfkg ++pgitlrd vnaipy+aik+glltv kk+kvn+fngrile+eglp+l veq f
NCBI__GCF_000020385.1:WP_012469942.1 510 MGFMPLDMPESVLVRFKGTFNPGITLRDAVNAIPYWAIKQGLLTVPKKNKVNIFNGRILEMEGLPELTVEQGF 582
************************************************************************* PP
TIGR00117 584 eltdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaey 656
eltda+aersaa+ i+l+ke+v+ yl+sn+ l+k+mia+gy+d +tl++rida+++wl+np+llead +aey
NCBI__GCF_000020385.1:WP_012469942.1 583 ELTDAAAERSAAAGCIQLSKESVATYLRSNVALMKKMIADGYQDPQTLQNRIDAVNEWLKNPQLLEADKNAEY 655
************************************************************************* PP
TIGR00117 657 aavieidlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraagkileaak.tvkarlwvvp 728
aavieidlaei+epila+pndpddvkllsevag i++vfigscmtnighfraa++i +++k + + r w++p
NCBI__GCF_000020385.1:WP_012469942.1 656 AAVIEIDLAEITEPILACPNDPDDVKLLSEVAGTPIQDVFIGSCMTNIGHFRAAAEIWKGEKfNPNVRTWITP 728
*************************************************************988899****** PP
TIGR00117 729 ptrmdeqqlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaa 801
ptrmd + l++e +++i++a gar+e+ gcslcmgnqarv dg+ +fststrnfd+r+g+gakv+lgsael+a
NCBI__GCF_000020385.1:WP_012469942.1 729 PTRMDSDLLKDEAVFSIYSAFGARIEIAGCSLCMGNQARVPDGVNMFSTSTRNFDDRIGNGAKVFLGSAELGA 801
************************************************************************* PP
TIGR00117 802 vaallgkiptkeeylalvsekvesakdklyrylnfnelenfe 843
vaa +gk+pt+ e+la+ ekv+++k+k+yryl+f+e+e ++
NCBI__GCF_000020385.1:WP_012469942.1 802 VAAKMGKLPTPAEFLAIYNEKVAPNKEKIYRYLQFDEMEGYK 843
**************************************9985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (843 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 25.13
//
[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