Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_008623754.1 C943_RS02195 aconitate hydratase
Query= BRENDA::Q8RP87
(747 letters)
>NCBI__GCF_000330725.2:WP_008623754.1
Length = 753
Score = 1041 bits (2692), Expect = 0.0
Identities = 507/747 (67%), Positives = 595/747 (79%), Gaps = 2/747 (0%)
Query: 1 MVYDLNMLKNFYASYKGKMEHVRAALKRPLTLAEKILYTHLYNVADLKNYERGEDYVNFR 60
M +D+ M+K Y +Y ++ R A+ RPLTL EKILY HL A + Y+RG YV+F
Sbjct: 1 MAFDIEMIKAVYGNYPTRIAAARKAVGRPLTLTEKILYAHLTQGAATEAYQRGGSYVDFN 60
Query: 61 PDRVAMQDATAQMALLQFMNAGKEAVAVPSTVHCDHLIQAYRGAERDIETATQTNREVYD 120
PDRVAMQDATAQMALLQFM AG++ VAVPSTVHCDHLIQA GA+ D++ A NREVYD
Sbjct: 61 PDRVAMQDATAQMALLQFMQAGRDKVAVPSTVHCDHLIQAEIGADADLQKAKDKNREVYD 120
Query: 121 FLRDVSSRYGIGFWKPGAGIIHQVVLENYAFPGGMMVGTDSHTPNAGGLGMVAIGVGGAD 180
FL VS++YGIGFWKPGAGIIHQVVLENYAFPGGMM+GTDSHTPNAGGLGM+AIGVGGAD
Sbjct: 121 FLASVSNKYGIGFWKPGAGIIHQVVLENYAFPGGMMIGTDSHTPNAGGLGMIAIGVGGAD 180
Query: 181 AVDVMTGMEWELKMPKLIGVRLTGELNGWTAPKDVILKLAGILTVKGGTNAIIEYFGPGT 240
A DVM G+ WELK PKLIGVRLTG L+GWT+ KDVILK+AGILTVKGGT A++EYFG G
Sbjct: 181 ACDVMAGLPWELKFPKLIGVRLTGRLSGWTSAKDVILKVAGILTVKGGTGAVVEYFGEGA 240
Query: 241 ASLSATGKATICNMGAEVGATTSLFPYDERMAVYLKATGREEVAAMADSVAADLRADDEV 300
SLSATGK TICNMGAE+GATTS+F YDE+ YL+ T R E+A MA+S+ L D EV
Sbjct: 241 RSLSATGKGTICNMGAEIGATTSIFGYDEKSEAYLRGTDRAEIAEMANSIKEHLTGDAEV 300
Query: 301 MARPDDFYDRVIEINLSELEPYINGPFTPDAATPISEFAEKVVTNGYPRKMEVGLIGSCT 360
A P+ ++D+VI+INLSELEP+INGPFTPD A P+S+FA+ V NG+P K+EVGLIGSCT
Sbjct: 301 YANPEKYFDQVIDINLSELEPHINGPFTPDLAWPLSKFAQAVKENGWPAKLEVGLIGSCT 360
Query: 361 NSSYQDISRAVSVARQVNEKNLGVAAPLIVNPGSEQIRATAERDGMMDVFEKMGATIMAN 420
NSSY+DISRA S+A+Q +K L + + PGSEQ+R T ERDG + VFEKMG ++AN
Sbjct: 361 NSSYEDISRAASLAQQAVDKKLIAKSEYTITPGSEQVRFTVERDGFLGVFEKMGGVVLAN 420
Query: 421 ACGPCIGQWKRHTDDPTRKNSIVTSFNRNFAKRADGNPNTFAFVASPEIVLALTIAGDLC 480
ACGPCIGQW RH + KNSI+TSFNRNFAKRADGNPNT AFVASPEIV A+ I+GDL
Sbjct: 421 ACGPCIGQWARHGAEKQEKNSIITSFNRNFAKRADGNPNTHAFVASPEIVTAMAISGDLT 480
Query: 481 FNPLKDRLVNHDGEKVKLSEPQGDELPSAGFVAGNQGYQAPG--GEKNEIRVAPDSQRLQ 538
FNP+ D L+N +G+ VKL EP+G ELP+ GF + GYQAP G K ++ V P S RLQ
Sbjct: 481 FNPVTDTLINEEGKAVKLDEPKGLELPTKGFAVEDAGYQAPASDGSKVQVIVDPKSDRLQ 540
Query: 539 LLTPFPAWDGNDFLNMPLLIKAQGKCTTDHISMAGPWLRFRGHLENISDNMLMGAVNAFN 598
LL PFPAW+G D + LLIKA+GKCTTDHISMAGPWLRFRGHL+NIS+NML+GAVNA+N
Sbjct: 541 LLAPFPAWEGTDLKGLKLLIKAKGKCTTDHISMAGPWLRFRGHLDNISNNMLIGAVNAYN 600
Query: 599 GETNKVWNRLTNTYETVSGTAKQYKADGISSIVVAEENYGEGSSREHAAMEPRFLHVKVI 658
GETNKV N+L Y V +QYKA GI SIVV +ENYGEGSSREHAAMEPRFL V+ I
Sbjct: 601 GETNKVKNQLGGGYGEVPAVQRQYKAHGIGSIVVGDENYGEGSSREHAAMEPRFLGVRAI 660
Query: 659 LAKSFARIHETNLKKQGMLAVTFADKADYDRIREHDLISVVGLKEFSPGRNLEVILHHED 718
L KSFARIHETNLKKQGMLA+TFA+ ADYD I+E D I ++GL +F+PG+ L V+LHH D
Sbjct: 661 LVKSFARIHETNLKKQGMLALTFANPADYDLIQEDDSIDILGLTDFAPGKPLTVVLHHAD 720
Query: 719 GTEERFAVQHTYNEQQIGWFRAGSALN 745
G++ V HTYNE QIGWFRAGSALN
Sbjct: 721 GSKNEIKVNHTYNEGQIGWFRAGSALN 747
Lambda K H
0.317 0.134 0.395
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: 1539
Number of extensions: 54
Number of successful extensions: 2
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: 747
Length of database: 753
Length adjustment: 40
Effective length of query: 707
Effective length of database: 713
Effective search space: 504091
Effective search space used: 504091
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: 55 (25.8 bits)
Align candidate WP_008623754.1 C943_RS02195 (aconitate hydratase)
to HMM TIGR01340 (aconitate hydratase, mitochondrial (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/TIGR01340.hmm
# target sequence database: /tmp/gapView.1437006.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Query: TIGR01340 [M=745]
Accession: TIGR01340
Description: aconitase_mito: aconitate hydratase, mitochondrial
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 1168.6 0.1 0 1168.4 0.1 1.0 1 NCBI__GCF_000330725.2:WP_008623754.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000330725.2:WP_008623754.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1168.4 0.1 0 0 6 745 .] 17 749 .. 12 749 .. 0.97
Alignments for each domain:
== domain 1 score: 1168.4 bits; conditional E-value: 0
TIGR01340 6 ekldkvrrvlnsrpltlaekvlyshlddpeesllsqdiedvrGksylklkpdrvamqdasaqmallqflsagl 78
+++ r+ ++ rpltl+ek+ly+hl++ + ++ + rG sy+ ++pdrvamqda+aqmallqf+ ag
NCBI__GCF_000330725.2:WP_008623754.1 17 TRIAAARKAVG-RPLTLTEKILYAHLTQGAA---TEAYQ--RGGSYVDFNPDRVAMQDATAQMALLQFMQAGR 83
56667788888.**************99888...55555..******************************** PP
TIGR01340 79 kkvavpasvhcdhlivakkGeekdlarakelnkevfdflesaakkygidfwkpGsGiihqivlenyavpGllm 151
+kvavp++vhcdhli+a++G++ dl++ak+ n+ev+dfl+s+++kygi+fwkpG+Giihq+vlenya+pG++m
NCBI__GCF_000330725.2:WP_008623754.1 84 DKVAVPSTVHCDHLIQAEIGADADLQKAKDKNREVYDFLASVSNKYGIGFWKPGAGIIHQVVLENYAFPGGMM 156
************************************************************************* PP
TIGR01340 152 lGtdshtpnaGGlaaiaiGvGGadavdvlagipwelkapkvlGvkltGklsgwtspkdvilklaglltvkGGt 224
+GtdshtpnaGGl++iaiGvGGada dv+ag+pwelk pk++Gv+ltG+lsgwts+kdvilk+ag+ltvkGGt
NCBI__GCF_000330725.2:WP_008623754.1 157 IGTDSHTPNAGGLGMIAIGVGGADACDVMAGLPWELKFPKLIGVRLTGRLSGWTSAKDVILKVAGILTVKGGT 229
************************************************************************* PP
TIGR01340 225 GaiveyfGeGveslsctGmaticnmGaeiGattslfpfneaskdylkatnraeiaeeakvakdka...ellka 294
Ga+veyfGeG sls tG +ticnmGaeiGatts+f ++e+s+ yl+ t+raeiae a+ k++ + a
NCBI__GCF_000330725.2:WP_008623754.1 230 GAVVEYFGEGARSLSATGKGTICNMGAEIGATTSIFGYDEKSEAYLRGTDRAEIAEMANSIKEHLtgdAEVYA 302
**********************************************************966655411134457 PP
TIGR01340 295 dkdaeydelieidlsklephvnGpftpdlstpiskfkekvkkekwpeklkvGliGsctnssyedmsrvasivk 367
+ + +d++i+i+ls+leph+nGpftpdl+ p+skf+++vk+++wp kl+vGliGsctnssyed+sr+as+++
NCBI__GCF_000330725.2:WP_008623754.1 303 NPEKYFDQVIDINLSELEPHINGPFTPDLAWPLSKFAQAVKENGWPAKLEVGLIGSCTNSSYEDISRAASLAQ 375
788899******************************************************************* PP
TIGR01340 368 daekaGlkskidftvtpGseqiratlerdgilevfekaGgvvlanacGpciGqwdrkdvvkkgekntiltsyn 440
+a ++ l +k+++t+tpGseq+r t+erdg l vfek+GgvvlanacGpciGqw r+ +k+ekn+i+ts+n
NCBI__GCF_000330725.2:WP_008623754.1 376 QAVDKKLIAKSEYTITPGSEQVRFTVERDGFLGVFEKMGGVVLANACGPCIGQWARHG-AEKQEKNSIITSFN 447
*********************************************************9.99************ PP
TIGR01340 441 rnfrgrndanratmaflaspelvtalsvaGslkfnpltdslktkdGkefklkapkGdelpekgfeaGrdtfqa 513
rnf r d+n++t+af+aspe+vta++++G+l+fnp+td+l +++Gk kl+ pkG elp+kgf +qa
NCBI__GCF_000330725.2:WP_008623754.1 448 RNFAKRADGNPNTHAFVASPEIVTAMAISGDLTFNPVTDTLINEEGKAVKLDEPKGLELPTKGFAVEDAGYQA 520
************************************************************************* PP
TIGR01340 514 esdspdenvevavdpksdrlqllepfekwngkdlkglrvlikvkGkcttdhisaaGpwlkykGhldnisentl 586
++++ ++v+v vdpksdrlqll+pf +w+g dlkgl++lik kGkcttdhis+aGpwl+++Ghldnis+n+l
NCBI__GCF_000330725.2:WP_008623754.1 521 PASD-GSKVQVIVDPKSDRLQLLAPFPAWEGTDLKGLKLLIKAKGKCTTDHISMAGPWLRFRGHLDNISNNML 592
*999.9******************************************************************* PP
TIGR01340 587 igavnaetgevnkvkdk.dGskgavpelakdykargvkwvvvaeenyGeGsarehaaleprylGgriiivksf 658
igavna +ge nkvk++ G +g+vp++ ++yka+g+ +vv++enyGeGs+rehaa+epr+lG r+i+vksf
NCBI__GCF_000330725.2:WP_008623754.1 593 IGAVNAYNGETNKVKNQlGGGYGEVPAVQRQYKAHGIGSIVVGDENYGEGSSREHAAMEPRFLGVRAILVKSF 665
*****************8999**************************************************** PP
TIGR01340 659 arihetnlkkqGvlpltfaneadydkiqaedkvellnlkellknnngkevdlrvkkkngkvveiklkhtlskd 731
arihetnlkkqG+l ltfan+adyd+iq +d++++l+l+++++ gk++++ +++ +g+ eik++ht ++
NCBI__GCF_000330725.2:WP_008623754.1 666 ARIHETNLKKQGMLALTFANPADYDLIQEDDSIDILGLTDFAP---GKPLTVVLHHADGSKNEIKVNHTYNEG 735
******************************************9...*************************** PP
TIGR01340 732 qieffkaGsalnll 745
qi++f+aGsalnl+
NCBI__GCF_000330725.2:WP_008623754.1 736 QIGWFRAGSALNLI 749
************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (745 nodes)
Target sequences: 1 (753 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: 27.28
//
[ok]
This GapMind analysis is from Sep 24 2021. 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