Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_053974641.1 I602_RS10500 aconitate hydratase
Query= BRENDA::Q8RP87
(747 letters)
>NCBI__GCF_001280865.1:WP_053974641.1
Length = 755
Score = 940 bits (2430), Expect = 0.0
Identities = 472/749 (63%), Positives = 565/749 (75%), Gaps = 5/749 (0%)
Query: 1 MVYDLNMLKNFYASYKGKMEHVRAALKRPLTLAEKILYTHLYNVADLKNYERGEDYVNFR 60
M +D++M+K Y S +++ R +PLTLAEKILY+HL+ K +RG+DYV+F
Sbjct: 1 MAFDIDMIKKVYESMTERVDAARKITGKPLTLAEKILYSHLWEGNPTKELQRGKDYVDFA 60
Query: 61 PDRVAMQDATAQMALLQFMNAGKEAVAVPSTVHCDHLIQAYRGAERDIETATQTNREVYD 120
PDR+A QDATAQMALLQFM AGK VAVP+TVHCDHLIQA GA +D++ A T+ EV++
Sbjct: 61 PDRIACQDATAQMALLQFMQAGKAKVAVPTTVHCDHLIQAKEGAAKDLKHANNTSSEVFN 120
Query: 121 FLRDVSSRYGIGFWKPGAGIIHQVVLENYAFPGGMMVGTDSHTPNAGGLGMVAIGVGGAD 180
FL VS++YGIGFWKPGAGIIHQVVLENYAFPGGMM+GTDSHT NAGGLGMVAIGVGGAD
Sbjct: 121 FLESVSNKYGIGFWKPGAGIIHQVVLENYAFPGGMMIGTDSHTVNAGGLGMVAIGVGGAD 180
Query: 181 AVDVMTGMEWELKMPKLIGVRLTGELNGWTAPKDVILKLAGILTVKGGTNAIIEYFGPGT 240
AVDVM GM WELK PKLIGV+LTG+L+GWTAPKDVILK+A ILTVKGGT AI+EYFGPG
Sbjct: 181 AVDVMAGMAWELKFPKLIGVKLTGKLSGWTAPKDVILKVAEILTVKGGTGAIVEYFGPGA 240
Query: 241 ASLSATGKATICNMGAEVGATTSLFPYDERMAVYLKATGREEVAAMADSVAADLRADDEV 300
S+S TGK TICNMGAE+GATTS F YDE M YLKAT RE+VA A+ + L AD EV
Sbjct: 241 TSMSCTGKGTICNMGAEIGATTSTFGYDESMERYLKATDREDVANAANEIKEYLTADAEV 300
Query: 301 MARPDDFYDRVIEINLSELEPYINGPFTPDAATPI-SEFAEKVVTNGYPRKMEVGLIGSC 359
P+ ++D+VIEINLSEL P +NGPFTPD +T + SE EK N +P +E GLIGSC
Sbjct: 301 YENPEQYFDQVIEINLSELGPLLNGPFTPDLSTTVGSEMTEKANANDWPLTVEWGLIGSC 360
Query: 360 TNSSYQDISRAVSVARQVNEKNLGVAAPLIVNPGSEQIRATAERDGMMDVFEKMGATIMA 419
TNSSY+D+SRA S+A+Q +K L A +NPGSEQ+R TAERDG++ +FE + A I
Sbjct: 361 TNSSYEDLSRASSIAQQAIDKGLKTKAEFGINPGSEQVRYTAERDGILQIFENLDAKIFT 420
Query: 420 NACGPCIGQWKRHTDDPTR-KNSIVTSFNRNFAKRADGNPNTFAFVASPEIVLALTIAGD 478
NACGPCIGQW R++D KNSIV SFNRNFAKRADGNPNT AFVASPEI A+ IAG
Sbjct: 421 NACGPCIGQWARYSDPKNAPKNSIVHSFNRNFAKRADGNPNTHAFVASPEITAAIAIAGR 480
Query: 479 LCFNPLKDRLVNHDGEKVKLSEPQGDELPSAGFVAGNQGYQAP--GGEKNEIRVAPDSQR 536
L FNPLKD+L+N DGE+V EP G ELP GF GY AP G + V DS+R
Sbjct: 481 LDFNPLKDKLINEDGEEVMFDEPTGWELPPKGFEVKENGYLAPDEDGSGVVVSVNDDSER 540
Query: 537 LQLLTPFPAWDGNDFLNMPLLIKAQGKCTTDHISMAGPWLRFRGHLENISDNMLMGAVNA 596
LQLLTPF G+ LLIKA GKCTTDHISMAGPWLRFRGHL+NI++N L+GAVNA
Sbjct: 541 LQLLTPFTPL-GSTITGAKLLIKAFGKCTTDHISMAGPWLRFRGHLDNIANNTLIGAVNA 599
Query: 597 FNGETNKVWNRLTNTYETVSGTAKQYKADGISSIVVAEENYGEGSSREHAAMEPRFLHVK 656
FN +TN V N+LT Y+ V ++YK +GI +IVV + NYGEGSSREHAAM+PR L V
Sbjct: 600 FNKKTNFVKNQLTGEYDAVPAVQREYKKEGIKTIVVGDHNYGEGSSREHAAMQPRHLGVA 659
Query: 657 VILAKSFARIHETNLKKQGMLAVTFADKADYDRIREHDLISVVGLKEFSPGRNLEVILHH 716
++ KSFARIHETNLKKQGML +TFA++ADYD I+E D + L EF+P + L + + H
Sbjct: 660 AVIVKSFARIHETNLKKQGMLGLTFANEADYDLIQEDDTFNFTDLNEFAPDKQLTLEIVH 719
Query: 717 EDGTEERFAVQHTYNEQQIGWFRAGSALN 745
+DG+ + + HTYN+ QI W+ GSALN
Sbjct: 720 KDGSSDTIKLNHTYNKAQIDWYNEGSALN 748
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: 1525
Number of extensions: 60
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: 747
Length of database: 755
Length adjustment: 40
Effective length of query: 707
Effective length of database: 715
Effective search space: 505505
Effective search space used: 505505
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_053974641.1 I602_RS10500 (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.4098004.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 1092.3 1.0 0 1092.1 1.0 1.0 1 NCBI__GCF_001280865.1:WP_053974641.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001280865.1:WP_053974641.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1092.1 1.0 0 0 1 745 [] 12 750 .. 12 750 .. 0.97
Alignments for each domain:
== domain 1 score: 1092.1 bits; conditional E-value: 0
TIGR01340 1 yekllekldkvrrvlnsrpltlaekvlyshlddpeesllsqdiedvrGksylklkpdrvamqdasaqmallqf 73
ye ++e++d r++++ +pltlaek+lyshl + + +++++ rGk y+ + pdr+a+qda+aqmallqf
NCBI__GCF_001280865.1:WP_053974641.1 12 YESMTERVDAARKITG-KPLTLAEKILYSHLWEGNP---TKELQ--RGKDYVDFAPDRIACQDATAQMALLQF 78
899************9.**************99988...67777..*************************** PP
TIGR01340 74 lsaglkkvavpasvhcdhlivakkGeekdlarakelnkevfdflesaakkygidfwkpGsGiihqivlenyav 146
+ ag kvavp++vhcdhli+ak+G+ kdl++a+++ evf+fles+++kygi+fwkpG+Giihq+vlenya+
NCBI__GCF_001280865.1:WP_053974641.1 79 MQAGKAKVAVPTTVHCDHLIQAKEGAAKDLKHANNTSSEVFNFLESVSNKYGIGFWKPGAGIIHQVVLENYAF 151
************************************************************************* PP
TIGR01340 147 pGllmlGtdshtpnaGGlaaiaiGvGGadavdvlagipwelkapkvlGvkltGklsgwtspkdvilklagllt 219
pG++m+Gtdsht naGGl+++aiGvGGadavdv+ag+ welk pk++GvkltGklsgwt+pkdvilk+a++lt
NCBI__GCF_001280865.1:WP_053974641.1 152 PGGMMIGTDSHTVNAGGLGMVAIGVGGADAVDVMAGMAWELKFPKLIGVKLTGKLSGWTAPKDVILKVAEILT 224
************************************************************************* PP
TIGR01340 220 vkGGtGaiveyfGeGveslsctGmaticnmGaeiGattslfpfneaskdylkatnraeiaeeakvakd...ka 289
vkGGtGaiveyfG+G s+sctG +ticnmGaeiGatts+f ++e++++ylkat+r+++a++a+ k+ +
NCBI__GCF_001280865.1:WP_053974641.1 225 VKGGTGAIVEYFGPGATSMSCTGKGTICNMGAEIGATTSTFGYDESMERYLKATDREDVANAANEIKEyltAD 297
**************************************************************99433311112 PP
TIGR01340 290 ellkadkdaeydelieidlsklephvnGpftpdlstpi.skfkekvkkekwpeklkvGliGsctnssyedmsr 361
+ ++ + +d++iei+ls+l p +nGpftpdlst + s+++ek+++++wp ++ GliGsctnssyed+sr
NCBI__GCF_001280865.1:WP_053974641.1 298 AEVYENPEQYFDQVIEINLSELGPLLNGPFTPDLSTTVgSEMTEKANANDWPLTVEWGLIGSCTNSSYEDLSR 370
22334555668************************999789******************************** PP
TIGR01340 362 vasivkdaekaGlkskidftvtpGseqiratlerdgilevfekaGgvvlanacGpciGqwdrkdvvkkgeknt 434
++si+++a ++Glk+k++f + pGseq+r t erdgil++fe+ +++++nacGpciGqw r + k+ kn+
NCBI__GCF_001280865.1:WP_053974641.1 371 ASSIAQQAIDKGLKTKAEFGINPGSEQVRYTAERDGILQIFENLDAKIFTNACGPCIGQWARYSDPKNAPKNS 443
****************************************************************9******** PP
TIGR01340 435 iltsynrnfrgrndanratmaflaspelvtalsvaGslkfnpltdslktkdGkefklkapkGdelpekgfeaG 507
i+ s+nrnf r d+n++t+af+aspe+ +a+++aG+l+fnpl d+l ++dG e ++ p+G elp kgfe
NCBI__GCF_001280865.1:WP_053974641.1 444 IVHSFNRNFAKRADGNPNTHAFVASPEITAAIAIAGRLDFNPLKDKLINEDGEEVMFDEPTGWELPPKGFEVK 516
************************************************************************* PP
TIGR01340 508 rdtfqaesdspdenvevavdpksdrlqllepfekwngkdlkglrvlikvkGkcttdhisaaGpwlkykGhldn 580
++ + a+ ++ + v v+v+ +s+rlqll pf + g+ ++g ++lik Gkcttdhis+aGpwl+++Ghldn
NCBI__GCF_001280865.1:WP_053974641.1 517 ENGYLAPDED-GSGVVVSVNDDSERLQLLTPFTPL-GSTITGAKLLIKAFGKCTTDHISMAGPWLRFRGHLDN 587
******9999.99*********************8.789********************************** PP
TIGR01340 581 isentligavnaetgevnkvkdk.dGskgavpelakdykargvkwvvvaeenyGeGsarehaaleprylGgri 652
i++ntligavna + + n vk++ +G++ avp++ ++yk++g+k +vv+++nyGeGs+rehaa++pr+lG +
NCBI__GCF_001280865.1:WP_053974641.1 588 IANNTLIGAVNAFNKKTNFVKNQlTGEYDAVPAVQREYKKEGIKTIVVGDHNYGEGSSREHAAMQPRHLGVAA 660
***********************9************************************************* PP
TIGR01340 653 iivksfarihetnlkkqGvlpltfaneadydkiqaedkvellnlkellknnngkevdlrvkkkngkvveiklk 725
+ivksfarihetnlkkqG+l ltfaneadyd+iq +d+ + +l+e+++ +k+++l++ +k+g++ +ikl+
NCBI__GCF_001280865.1:WP_053974641.1 661 VIVKSFARIHETNLKKQGMLGLTFANEADYDLIQEDDTFNFTDLNEFAP---DKQLTLEIVHKDGSSDTIKLN 730
*************************************999999999988...9******************** PP
TIGR01340 726 htlskdqieffkaGsalnll 745
ht +k qi+++++Gsalnl+
NCBI__GCF_001280865.1:WP_053974641.1 731 HTYNKAQIDWYNEGSALNLI 750
******************86 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (745 nodes)
Target sequences: 1 (755 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: 00:00:00.03
# Mc/sec: 16.75
//
[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