Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate 351600 BT2072 aconitate hydratase (NCBI ptt file)
Query= BRENDA::Q8RP87 (747 letters) >FitnessBrowser__Btheta:351600 Length = 747 Score = 1314 bits (3401), Expect = 0.0 Identities = 635/747 (85%), Positives = 691/747 (92%) Query: 1 MVYDLNMLKNFYASYKGKMEHVRAALKRPLTLAEKILYTHLYNVADLKNYERGEDYVNFR 60 MVYDL ML+ FY++YKGK+EHVRA LKRPLTLAEKILY HL+N DLKNY+RGEDYVNFR Sbjct: 1 MVYDLTMLEAFYSAYKGKVEHVRAVLKRPLTLAEKILYAHLFNEGDLKNYKRGEDYVNFR 60 Query: 61 PDRVAMQDATAQMALLQFMNAGKEAVAVPSTVHCDHLIQAYRGAERDIETATQTNREVYD 120 PDRVAMQDATAQMALLQFMNAGKE VAVPSTVHCDHLIQAY+GA+ DI TAT+TN EVYD Sbjct: 61 PDRVAMQDATAQMALLQFMNAGKEKVAVPSTVHCDHLIQAYKGAKEDIATATKTNEEVYD 120 Query: 121 FLRDVSSRYGIGFWKPGAGIIHQVVLENYAFPGGMMVGTDSHTPNAGGLGMVAIGVGGAD 180 FLRDVSSRYGIGFWKPGAGIIHQVVLENYAFPGGMMVGTDSHTPNAGGLGMVAIGVGGAD Sbjct: 121 FLRDVSSRYGIGFWKPGAGIIHQVVLENYAFPGGMMVGTDSHTPNAGGLGMVAIGVGGAD 180 Query: 181 AVDVMTGMEWELKMPKLIGVRLTGELNGWTAPKDVILKLAGILTVKGGTNAIIEYFGPGT 240 AVDVMTGMEWELKMP++IGVRLTG+L+GWT+PKDVILKLAGILTVKGGTN+IIEYFGPGT Sbjct: 181 AVDVMTGMEWELKMPRIIGVRLTGKLSGWTSPKDVILKLAGILTVKGGTNSIIEYFGPGT 240 Query: 241 ASLSATGKATICNMGAEVGATTSLFPYDERMAVYLKATGREEVAAMADSVAADLRADDEV 300 ASLSATGKATICNMGAEVGATTSLFP+D RMA YL+ATGR+ + +A++V +LRAD +V Sbjct: 241 ASLSATGKATICNMGAEVGATTSLFPFDGRMATYLRATGRDRIVELAEAVDCELRADQQV 300 Query: 301 MARPDDFYDRVIEINLSELEPYINGPFTPDAATPISEFAEKVVTNGYPRKMEVGLIGSCT 360 P+ +YDRVI+I+LS LEPYINGPFTPDAATPISEFAEKV+ NGYPRKMEVGLIGSCT Sbjct: 301 TDEPEKYYDRVIDIDLSTLEPYINGPFTPDAATPISEFAEKVLLNGYPRKMEVGLIGSCT 360 Query: 361 NSSYQDISRAVSVARQVNEKNLGVAAPLIVNPGSEQIRATAERDGMMDVFEKMGATIMAN 420 NSSYQD+SRA S+ARQV EKNL VA+PLI+NPGSEQIRATAERDGMMD F ++GA IMAN Sbjct: 361 NSSYQDLSRAASLARQVKEKNLSVASPLIINPGSEQIRATAERDGMMDDFMQIGAVIMAN 420 Query: 421 ACGPCIGQWKRHTDDPTRKNSIVTSFNRNFAKRADGNPNTFAFVASPEIVLALTIAGDLC 480 ACGPCIGQWKRHTDDPTRKNSIVTSFNRNFAKRADGNPNT+AFVASPE+ +ALTIAGDLC Sbjct: 421 ACGPCIGQWKRHTDDPTRKNSIVTSFNRNFAKRADGNPNTYAFVASPELTMALTIAGDLC 480 Query: 481 FNPLKDRLVNHDGEKVKLSEPQGDELPSAGFVAGNQGYQAPGGEKNEIRVAPDSQRLQLL 540 FNPLKDRL+NHDGEKVKL+EP GDELP GF +GN+GY PGG K I V P SQRLQLL Sbjct: 481 FNPLKDRLMNHDGEKVKLAEPVGDELPLRGFTSGNEGYITPGGTKTAINVNPASQRLQLL 540 Query: 541 TPFPAWDGNDFLNMPLLIKAQGKCTTDHISMAGPWLRFRGHLENISDNMLMGAVNAFNGE 600 TPFPAWDG D LNMPLLIKAQGKCTTDHISMAGPWLRFRGHLENISDNMLMGAVNAFNGE Sbjct: 541 TPFPAWDGQDILNMPLLIKAQGKCTTDHISMAGPWLRFRGHLENISDNMLMGAVNAFNGE 600 Query: 601 TNKVWNRLTNTYETVSGTAKQYKADGISSIVVAEENYGEGSSREHAAMEPRFLHVKVILA 660 TN VWNR TNTY TVSGTAK YK++GI SIVVAEENYGEGSSREHAAMEPRFL+V+VILA Sbjct: 601 TNNVWNRSTNTYGTVSGTAKMYKSEGIPSIVVAEENYGEGSSREHAAMEPRFLNVRVILA 660 Query: 661 KSFARIHETNLKKQGMLAVTFADKADYDRIREHDLISVVGLKEFSPGRNLEVILHHEDGT 720 KSFARIHETNLKKQGMLA+TFADKADYD+I+EHDL+SV+GL +F+PGRNL V+LHHEDGT Sbjct: 661 KSFARIHETNLKKQGMLALTFADKADYDKIQEHDLLSVIGLPDFAPGRNLTVVLHHEDGT 720 Query: 721 EERFAVQHTYNEQQIGWFRAGSALNAK 747 +E F QHTYNEQQI WFRAGSALNA+ Sbjct: 721 KESFEAQHTYNEQQIAWFRAGSALNAR 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: 1749 Number of extensions: 51 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: 747 Length adjustment: 40 Effective length of query: 707 Effective length of database: 707 Effective search space: 499849 Effective search space used: 499849 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 351600 BT2072 (aconitate hydratase (NCBI ptt file))
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.1795098.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 1094.6 0.0 0 1094.4 0.0 1.0 1 FitnessBrowser__Btheta:351600 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Btheta:351600 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1094.4 0.0 0 0 3 744 .. 14 746 .. 12 747 .] 0.97 Alignments for each domain: == domain 1 score: 1094.4 bits; conditional E-value: 0 TIGR01340 3 kllekldkvrrvlnsrpltlaekvlyshlddpeesllsqdiedvrGksylklkpdrvamqdasaqmallqflsaglkkva 82 + k+++vr vl+ rpltlaek+ly+hl + + ++ + rG+ y++++pdrvamqda+aqmallqf+ ag +kva FitnessBrowser__Btheta:351600 14 AYKGKVEHVRAVLK-RPLTLAEKILYAHLFNEGD---LKNYK--RGEDYVNFRPDRVAMQDATAQMALLQFMNAGKEKVA 87 5667899******9.***************9988...45566..9*********************************** PP TIGR01340 83 vpasvhcdhlivakkGeekdlarakelnkevfdflesaakkygidfwkpGsGiihqivlenyavpGllmlGtdshtpnaG 162 vp++vhcdhli+a kG+++d+a+a+++n+ev+dfl ++ +ygi+fwkpG+Giihq+vlenya+pG++m+GtdshtpnaG FitnessBrowser__Btheta:351600 88 VPSTVHCDHLIQAYKGAKEDIATATKTNEEVYDFLRDVSSRYGIGFWKPGAGIIHQVVLENYAFPGGMMVGTDSHTPNAG 167 ******************************************************************************** PP TIGR01340 163 GlaaiaiGvGGadavdvlagipwelkapkvlGvkltGklsgwtspkdvilklaglltvkGGtGaiveyfGeGveslsctG 242 Gl+++aiGvGGadavdv++g+ welk p+++Gv+ltGklsgwtspkdvilklag+ltvkGGt i+eyfG+G sls tG FitnessBrowser__Btheta:351600 168 GLGMVAIGVGGADAVDVMTGMEWELKMPRIIGVRLTGKLSGWTSPKDVILKLAGILTVKGGTNSIIEYFGPGTASLSATG 247 ******************************************************************************** PP TIGR01340 243 maticnmGaeiGattslfpfneaskdylkatnraeiaeeak...vakdkaellkadkdaeydelieidlsklephvnGpf 319 aticnmGae+Gattslfpf+ +++ yl+at+r++i e a+ + + + + ++ + yd++i+idls+lep++nGpf FitnessBrowser__Btheta:351600 248 KATICNMGAEVGATTSLFPFDGRMATYLRATGRDRIVELAEavdCELRADQQVTDEPEKYYDRVIDIDLSTLEPYINGPF 327 ************************************9998833233344455555557789******************* PP TIGR01340 320 tpdlstpiskfkekvkkekwpeklkvGliGsctnssyedmsrvasivkdaekaGlkskidftvtpGseqiratlerdgil 399 tpd +tpis+f+ekv +++p+k++vGliGsctnssy+d+sr+as++++ +++ l ++++ + pGseqirat erdg++ FitnessBrowser__Btheta:351600 328 TPDAATPISEFAEKVLLNGYPRKMEVGLIGSCTNSSYQDLSRAASLARQVKEKNLSVASPLIINPGSEQIRATAERDGMM 407 ******************************************************************************** PP TIGR01340 400 evfekaGgvvlanacGpciGqwdrkdvvkkgekntiltsynrnfrgrndanratmaflaspelvtalsvaGslkfnpltd 479 + f + G+v++anacGpciGqw+r+ kn+i+ts+nrnf r d+n++t+af+aspel +al++aG+l fnpl d FitnessBrowser__Btheta:351600 408 DDFMQIGAVIMANACGPCIGQWKRHT-DDPTRKNSIVTSFNRNFAKRADGNPNTYAFVASPELTMALTIAGDLCFNPLKD 486 ************************98.456789*********************************************** PP TIGR01340 480 slktkdGkefklkapkGdelpekgfeaGrdtfqaesdspdenvevavdpksdrlqllepfekwngkdlkglrvlikvkGk 559 l ++dG + kl+ p Gdelp +gf +G++ + ++ ++ + ++v+p s+rlqll pf +w+g+d+ ++++lik +Gk FitnessBrowser__Btheta:351600 487 RLMNHDGEKVKLAEPVGDELPLRGFTSGNEGYITPGGT---KTAINVNPASQRLQLLTPFPAWDGQDILNMPLLIKAQGK 563 ********************************999887...6678899******************************** PP TIGR01340 560 cttdhisaaGpwlkykGhldnisentligavnaetgevnkvkdk.dGskgavpelakdykargvkwvvvaeenyGeGsar 638 cttdhis+aGpwl+++Ghl+nis+n+l+gavna +ge n+v ++ + ++g+v ++ak yk++g++ +vvaeenyGeGs+r FitnessBrowser__Btheta:351600 564 CTTDHISMAGPWLRFRGHLENISDNMLMGAVNAFNGETNNVWNRsTNTYGTVSGTAKMYKSEGIPSIVVAEENYGEGSSR 643 ********************************************88999******************************* PP TIGR01340 639 ehaaleprylGgriiivksfarihetnlkkqGvlpltfaneadydkiqaedkvellnlkellknnngkevdlrvkkkngk 718 ehaa+epr+l r+i++ksfarihetnlkkqG+l ltfa++adydkiq +d +++++l ++++ g+++++ +++++g FitnessBrowser__Btheta:351600 644 EHAAMEPRFLNVRVILAKSFARIHETNLKKQGMLALTFADKADYDKIQEHDLLSVIGLPDFAP---GRNLTVVLHHEDGT 720 **************************************************************9...999*********** PP TIGR01340 719 vveiklkhtlskdqieffkaGsalnl 744 ++ ++ht +++qi +f+aGsaln FitnessBrowser__Btheta:351600 721 KESFEAQHTYNEQQIAWFRAGSALNA 746 ************************95 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (745 nodes) Target sequences: 1 (747 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: 00:00:00.02 # Mc/sec: 25.92 // [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