Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate Echvi_2531 Echvi_2531 aconitate hydratase, mitochondrial
Query= BRENDA::Q8RP87
(747 letters)
>FitnessBrowser__Cola:Echvi_2531
Length = 757
Score = 980 bits (2533), Expect = 0.0
Identities = 482/747 (64%), Positives = 578/747 (77%), Gaps = 2/747 (0%)
Query: 1 MVYDLNMLKNFYASYKGKMEHVRAALKRPLTLAEKILYTHLYNVADLKNYERGEDYVNFR 60
M +D+ M+K YA Y ++ R + +PLTLAEKILY HL+ + +ERG+ YV+F
Sbjct: 1 MAFDIEMIKAVYAKYPERIAAARKTVGKPLTLAEKILYAHLWGGDATQAFERGKSYVDFA 60
Query: 61 PDRVAMQDATAQMALLQFMNAGKEAVAVPSTVHCDHLIQAYRGAERDIETATQTNREVYD 120
PDRVAMQDATAQMALLQFM AGKE VAVPST HCDHLI A +GAE D+ ++ + EV++
Sbjct: 61 PDRVAMQDATAQMALLQFMQAGKEKVAVPSTAHCDHLILAQKGAEEDLRSSLTASGEVFN 120
Query: 121 FLRDVSSRYGIGFWKPGAGIIHQVVLENYAFPGGMMVGTDSHTPNAGGLGMVAIGVGGAD 180
FL VS++YGIGFWKPGAGIIHQVVLENYAFPGGMM+GTDSHT NAGGLGMVAIGVGGAD
Sbjct: 121 FLESVSNKYGIGFWKPGAGIIHQVVLENYAFPGGMMIGTDSHTVNAGGLGMVAIGVGGAD 180
Query: 181 AVDVMTGMEWELKMPKLIGVRLTGELNGWTAPKDVILKLAGILTVKGGTNAIIEYFGPGT 240
AVDVM GM WELK PKLIGV+LTG++NGWT+ KDVILK+AGILTVKGGT I+EYFG G
Sbjct: 181 AVDVMAGMPWELKFPKLIGVKLTGKMNGWTSAKDVILKVAGILTVKGGTGCIVEYFGEGA 240
Query: 241 ASLSATGKATICNMGAEVGATTSLFPYDERMAVYLKATGREEVAAMADSVAADLRADDEV 300
SLSATGK TICNMGAE+GATTS F YDE M YL++T R +VA +A+ V L DDEV
Sbjct: 241 KSLSATGKGTICNMGAEIGATTSTFGYDESMERYLRSTDRADVADLANEVKEHLTGDDEV 300
Query: 301 MARPDDFYDRVIEINLSELEPYINGPFTPDAATPISEFAEKVVTNGYPRKMEVGLIGSCT 360
A P+ ++D+VIEI+LS LEP+INGPFTPD ATP+S+ + NG+P K+E GLIGSCT
Sbjct: 301 YANPEQYFDQVIEIDLSTLEPHINGPFTPDRATPVSQIRAEAEKNGWPTKVEWGLIGSCT 360
Query: 361 NSSYQDISRAVSVARQVNEKNLGVAAPLIVNPGSEQIRATAERDGMMDVFEKMGATIMAN 420
NSSY+D+SRA S+A+Q +K L A +NPGSEQ+R TAERDGM+ +FE + ATI N
Sbjct: 361 NSSYEDLSRASSIAQQAVDKQLKTKADFGINPGSEQVRFTAERDGMLKIFEDLDATIFTN 420
Query: 421 ACGPCIGQWKRHTDDPTRKNSIVTSFNRNFAKRADGNPNTFAFVASPEIVLALTIAGDLC 480
ACGPCIGQW R D KN+IV SFNRNF+KRADGNPNT AFV SPE+V A+ I+GDL
Sbjct: 421 ACGPCIGQWARTGADKQEKNTIVHSFNRNFSKRADGNPNTHAFVTSPEMVAAIAISGDLG 480
Query: 481 FNPLKDRLVNHDGEKVKLSEPQGDELPSAGFVAGNQGYQAPG--GEKNEIRVAPDSQRLQ 538
FNPL D L N +GE+VKL P+G+ELP+ GF + GYQAP G E++V PDS+RLQ
Sbjct: 481 FNPLTDTLTNANGEEVKLDPPKGEELPAKGFAVEDNGYQAPAEDGSGIEVKVNPDSKRLQ 540
Query: 539 LLTPFPAWDGNDFLNMPLLIKAQGKCTTDHISMAGPWLRFRGHLENISDNMLMGAVNAFN 598
LLTPF WDG + LLIKA GKCTTDHISMAGPWLRFRGHL+NISDN L+GAVNAFN
Sbjct: 541 LLTPFEPWDGKNITGAKLLIKAFGKCTTDHISMAGPWLRFRGHLDNISDNCLIGAVNAFN 600
Query: 599 GETNKVWNRLTNTYETVSGTAKQYKADGISSIVVAEENYGEGSSREHAAMEPRFLHVKVI 658
ETN V ++LT Y V T + YKA GI +IVV + NYGEGSSREHAAMEPR L VK +
Sbjct: 601 EETNAVKSQLTGEYGPVPATQRAYKAAGIPTIVVGDHNYGEGSSREHAAMEPRHLGVKAV 660
Query: 659 LAKSFARIHETNLKKQGMLAVTFADKADYDRIREHDLISVVGLKEFSPGRNLEVILHHED 718
L KSFARIHETNLKKQGMLA+TF ++ADYD+++E D I+ + L +F+P + L + H D
Sbjct: 661 LVKSFARIHETNLKKQGMLALTFDNEADYDKVQEDDTINFLDLDQFAPDKPLTLEFVHAD 720
Query: 719 GTEERFAVQHTYNEQQIGWFRAGSALN 745
G+++ H+YN+ QI WF+AGSALN
Sbjct: 721 GSKDVIVANHSYNDAQIKWFKAGSALN 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: 1538
Number of extensions: 55
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: 757
Length adjustment: 40
Effective length of query: 707
Effective length of database: 717
Effective search space: 506919
Effective search space used: 506919
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 Echvi_2531 Echvi_2531 (aconitate hydratase, mitochondrial)
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.10201.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 1118.9 0.2 0 1118.7 0.2 1.0 1 lcl|FitnessBrowser__Cola:Echvi_2531 Echvi_2531 aconitate hydratase,
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cola:Echvi_2531 Echvi_2531 aconitate hydratase, mitochondrial
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1118.7 0.2 0 0 1 745 [] 12 749 .. 12 749 .. 0.97
Alignments for each domain:
== domain 1 score: 1118.7 bits; conditional E-value: 0
TIGR01340 1 yekllekldkvrrvlnsrpltlaekvlyshlddpeesllsqdiedvrGksylklkpdrvamqdasaqmallqfl 74
y+k e++ r+ ++ +pltlaek+ly+hl + +q e rGksy+ + pdrvamqda+aqmallqf+
lcl|FitnessBrowser__Cola:Echvi_2531 12 YAKYPERIAAARKTVG-KPLTLAEKILYAHLWGGDA---TQAFE--RGKSYVDFAPDRVAMQDATAQMALLQFM 79
7788889999999999.**************99988...78888..**************************** PP
TIGR01340 75 saglkkvavpasvhcdhlivakkGeekdlarakelnkevfdflesaakkygidfwkpGsGiihqivlenyavpG 148
ag +kvavp++ hcdhli a+kG+e+dl+++ evf+fles+++kygi+fwkpG+Giihq+vlenya+pG
lcl|FitnessBrowser__Cola:Echvi_2531 80 QAGKEKVAVPSTAHCDHLILAQKGAEEDLRSSLTASGEVFNFLESVSNKYGIGFWKPGAGIIHQVVLENYAFPG 153
************************************************************************** PP
TIGR01340 149 llmlGtdshtpnaGGlaaiaiGvGGadavdvlagipwelkapkvlGvkltGklsgwtspkdvilklaglltvkG 222
++m+Gtdsht naGGl+++aiGvGGadavdv+ag+pwelk pk++GvkltGk++gwts+kdvilk+ag+ltvkG
lcl|FitnessBrowser__Cola:Echvi_2531 154 GMMIGTDSHTVNAGGLGMVAIGVGGADAVDVMAGMPWELKFPKLIGVKLTGKMNGWTSAKDVILKVAGILTVKG 227
************************************************************************** PP
TIGR01340 223 GtGaiveyfGeGveslsctGmaticnmGaeiGattslfpfneaskdylkatnraeiaeeakvakdka...ellk 293
GtG iveyfGeG +sls tG +ticnmGaeiGatts+f ++e++++yl++t+ra++a+ a+ k++ + +
lcl|FitnessBrowser__Cola:Echvi_2531 228 GTGCIVEYFGEGAKSLSATGKGTICNMGAEIGATTSTFGYDESMERYLRSTDRADVADLANEVKEHLtgdDEVY 301
**********************************************************9995444431113444 PP
TIGR01340 294 adkdaeydelieidlsklephvnGpftpdlstpiskfkekvkkekwpeklkvGliGsctnssyedmsrvasivk 367
a+ + +d++ieidls+leph+nGpftpd +tp+s+++ +++k++wp+k++ GliGsctnssyed+sr++si++
lcl|FitnessBrowser__Cola:Echvi_2531 302 ANPEQYFDQVIEIDLSTLEPHINGPFTPDRATPVSQIRAEAEKNGWPTKVEWGLIGSCTNSSYEDLSRASSIAQ 375
6667789******************************************************************* PP
TIGR01340 368 daekaGlkskidftvtpGseqiratlerdgilevfekaGgvvlanacGpciGqwdrkdvvkkgekntiltsynr 441
+a ++ lk+k+df + pGseq+r t erdg+l++fe+ +++++nacGpciGqw r k+eknti+ s+nr
lcl|FitnessBrowser__Cola:Echvi_2531 376 QAVDKQLKTKADFGINPGSEQVRFTAERDGMLKIFEDLDATIFTNACGPCIGQWARTG-ADKQEKNTIVHSFNR 448
*********************************************************9.99************* PP
TIGR01340 442 nfrgrndanratmaflaspelvtalsvaGslkfnpltdslktkdGkefklkapkGdelpekgfeaGrdtfqaes 515
nf r d+n++t+af++spe+v+a++++G+l fnpltd+l++++G e kl++pkG+elp+kgf + +qa++
lcl|FitnessBrowser__Cola:Echvi_2531 449 NFSKRADGNPNTHAFVTSPEMVAAIAISGDLGFNPLTDTLTNANGEEVKLDPPKGEELPAKGFAVEDNGYQAPA 522
************************************************************************** PP
TIGR01340 516 dspdenvevavdpksdrlqllepfekwngkdlkglrvlikvkGkcttdhisaaGpwlkykGhldnisentliga 589
++ + +ev+v+p+s+rlqll pfe+w+gk+++g ++lik Gkcttdhis+aGpwl+++Ghldnis+n liga
lcl|FitnessBrowser__Cola:Echvi_2531 523 ED-GSGIEVKVNPDSKRLQLLTPFEPWDGKNITGAKLLIKAFGKCTTDHISMAGPWLRFRGHLDNISDNCLIGA 595
*9.9********************************************************************** PP
TIGR01340 590 vnaetgevnkvkdk.dGskgavpelakdykargvkwvvvaeenyGeGsarehaaleprylGgriiivksfarih 662
vna ++e n vk + +G++g vp++ + yka g++ +vv+++nyGeGs+rehaa+epr+lG ++++vksfarih
lcl|FitnessBrowser__Cola:Echvi_2531 596 VNAFNEETNAVKSQlTGEYGPVPATQRAYKAAGIPTIVVGDHNYGEGSSREHAAMEPRHLGVKAVLVKSFARIH 669
************999*********************************************************** PP
TIGR01340 663 etnlkkqGvlpltfaneadydkiqaedkvellnlkellknnngkevdlrvkkkngkvveiklkhtlskdqieff 736
etnlkkqG+l ltf neadydk+q +d+++ l+l ++++ +k+++l+ + +g+ i ++h+ ++ qi++f
lcl|FitnessBrowser__Cola:Echvi_2531 670 ETNLKKQGMLALTFDNEADYDKVQEDDTINFLDLDQFAP---DKPLTLEFVHADGSKDVIVANHSYNDAQIKWF 740
********************************9999999...9******************************* PP
TIGR01340 737 kaGsalnll 745
kaGsalnl+
lcl|FitnessBrowser__Cola:Echvi_2531 741 KAGSALNLI 749
*******86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (745 nodes)
Target sequences: 1 (757 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.04
# Mc/sec: 11.92
//
[ok]
This GapMind analysis is from Sep 17 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