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.12513.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: 0.03u 0.03s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 7.99
//
[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:

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:

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