Alignments for a candidate for acn in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Bacteroides thetaiotaomicron VPI-5482

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.12687.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  lcl|FitnessBrowser__Btheta:351600  BT2072 aconitate hydratase (NCBI


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Btheta:351600  BT2072 aconitate hydratase (NCBI ptt file)
   #    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 kllekldkvrrvlnsrpltlaekvlyshlddpeesllsqdiedvrGksylklkpdrvamqdasaqmallqflsagl 78 
                                          + k+++vr vl+ rpltlaek+ly+hl +  +    ++ +  rG+ y++++pdrvamqda+aqmallqf+ ag 
  lcl|FitnessBrowser__Btheta:351600  14 AYKGKVEHVRAVLK-RPLTLAEKILYAHLFNEGD---LKNYK--RGEDYVNFRPDRVAMQDATAQMALLQFMNAGK 83 
                                        5667899******9.***************9988...45566..9******************************* PP

                          TIGR01340  79 kkvavpasvhcdhlivakkGeekdlarakelnkevfdflesaakkygidfwkpGsGiihqivlenyavpGllmlGt 154
                                        +kvavp++vhcdhli+a kG+++d+a+a+++n+ev+dfl  ++ +ygi+fwkpG+Giihq+vlenya+pG++m+Gt
  lcl|FitnessBrowser__Btheta:351600  84 EKVAVPSTVHCDHLIQAYKGAKEDIATATKTNEEVYDFLRDVSSRYGIGFWKPGAGIIHQVVLENYAFPGGMMVGT 159
                                        **************************************************************************** PP

                          TIGR01340 155 dshtpnaGGlaaiaiGvGGadavdvlagipwelkapkvlGvkltGklsgwtspkdvilklaglltvkGGtGaivey 230
                                        dshtpnaGGl+++aiGvGGadavdv++g+ welk p+++Gv+ltGklsgwtspkdvilklag+ltvkGGt  i+ey
  lcl|FitnessBrowser__Btheta:351600 160 DSHTPNAGGLGMVAIGVGGADAVDVMTGMEWELKMPRIIGVRLTGKLSGWTSPKDVILKLAGILTVKGGTNSIIEY 235
                                        **************************************************************************** PP

                          TIGR01340 231 fGeGveslsctGmaticnmGaeiGattslfpfneaskdylkatnraeiaeeak...vakdkaellkadkdaeydel 303
                                        fG+G  sls tG aticnmGae+Gattslfpf+ +++ yl+at+r++i e a+   +   + + + ++ +  yd++
  lcl|FitnessBrowser__Btheta:351600 236 FGPGTASLSATGKATICNMGAEVGATTSLFPFDGRMATYLRATGRDRIVELAEavdCELRADQQVTDEPEKYYDRV 311
                                        ************************************************9998833233344455555557789*** PP

                          TIGR01340 304 ieidlsklephvnGpftpdlstpiskfkekvkkekwpeklkvGliGsctnssyedmsrvasivkdaekaGlkskid 379
                                        i+idls+lep++nGpftpd +tpis+f+ekv  +++p+k++vGliGsctnssy+d+sr+as++++ +++ l  +++
  lcl|FitnessBrowser__Btheta:351600 312 IDIDLSTLEPYINGPFTPDAATPISEFAEKVLLNGYPRKMEVGLIGSCTNSSYQDLSRAASLARQVKEKNLSVASP 387
                                        **************************************************************************** PP

                          TIGR01340 380 ftvtpGseqiratlerdgilevfekaGgvvlanacGpciGqwdrkdvvkkgekntiltsynrnfrgrndanratma 455
                                        + + pGseqirat erdg+++ f + G+v++anacGpciGqw+r+       kn+i+ts+nrnf  r d+n++t+a
  lcl|FitnessBrowser__Btheta:351600 388 LIINPGSEQIRATAERDGMMDDFMQIGAVIMANACGPCIGQWKRHT-DDPTRKNSIVTSFNRNFAKRADGNPNTYA 462
                                        ********************************************98.456789*********************** PP

                          TIGR01340 456 flaspelvtalsvaGslkfnpltdslktkdGkefklkapkGdelpekgfeaGrdtfqaesdspdenvevavdpksd 531
                                        f+aspel +al++aG+l fnpl d l ++dG + kl+ p Gdelp +gf +G++ + ++ ++   +  ++v+p s+
  lcl|FitnessBrowser__Btheta:351600 463 FVASPELTMALTIAGDLCFNPLKDRLMNHDGEKVKLAEPVGDELPLRGFTSGNEGYITPGGT---KTAINVNPASQ 535
                                        ********************************************************999887...6678899**** PP

                          TIGR01340 532 rlqllepfekwngkdlkglrvlikvkGkcttdhisaaGpwlkykGhldnisentligavnaetgevnkvkdk.dGs 606
                                        rlqll pf +w+g+d+ ++++lik +Gkcttdhis+aGpwl+++Ghl+nis+n+l+gavna +ge n+v ++ + +
  lcl|FitnessBrowser__Btheta:351600 536 RLQLLTPFPAWDGQDILNMPLLIKAQGKCTTDHISMAGPWLRFRGHLENISDNMLMGAVNAFNGETNNVWNRsTNT 611
                                        ************************************************************************8899 PP

                          TIGR01340 607 kgavpelakdykargvkwvvvaeenyGeGsarehaaleprylGgriiivksfarihetnlkkqGvlpltfaneady 682
                                        +g+v ++ak yk++g++ +vvaeenyGeGs+rehaa+epr+l  r+i++ksfarihetnlkkqG+l ltfa++ady
  lcl|FitnessBrowser__Btheta:351600 612 YGTVSGTAKMYKSEGIPSIVVAEENYGEGSSREHAAMEPRFLNVRVILAKSFARIHETNLKKQGMLALTFADKADY 687
                                        9*************************************************************************** PP

                          TIGR01340 683 dkiqaedkvellnlkellknnngkevdlrvkkkngkvveiklkhtlskdqieffkaGsalnl 744
                                        dkiq +d +++++l ++++   g+++++ +++++g  ++  ++ht +++qi +f+aGsaln 
  lcl|FitnessBrowser__Btheta:351600 688 DKIQEHDLLSVIGLPDFAP---GRNLTVVLHHEDGTKESFEAQHTYNEQQIAWFRAGSALNA 746
                                        ******************9...999***********************************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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.06
# Mc/sec: 7.97
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources