Alignments for a candidate for acn in Desulfovibrio vulgaris Miyazaki F

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Desulfovibrio vulgaris Miyazaki F

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate 8502313 DvMF_3021 aconitate hydratase (RefSeq)

Query= BRENDA::Q99798
         (780 letters)



>FitnessBrowser__Miya:8502313
          Length = 641

 Score =  347 bits (889), Expect = 2e-99
 Identities = 249/716 (34%), Positives = 356/716 (49%), Gaps = 84/716 (11%)

Query: 63  LTLSEKIVYGHLDDPASQEIERGKSYLRLRPDRVAMQDATAQMAMLQFISSGLSKVAVPS 122
           + L++KI+  HL    S E+  G   + LR D+   QDAT  MA LQF + G+ +V    
Sbjct: 3   MNLTQKIIAAHL---VSGEMAPGAE-IGLRIDQTLTQDATGTMAYLQFEAMGVDRVRTDL 58

Query: 123 TI-HCDHLIEAQVGGEKDLRRAKDINQEVYNFLATAGAKYGVGFWKPGSGIIHQIILENY 181
           ++ + DH    Q+G           N + + FL T  AK+GV F  PG+GI HQ+ LEN+
Sbjct: 59  SVSYVDHNT-LQMGFR---------NPDDHRFLRTVAAKHGVIFSPPGTGICHQLHLENF 108

Query: 182 AYPGVLLIGTDSHTPNGGGLGGICIGVGGADAVDVMAGIPWELKCPKVIGVKLTGSLSGW 241
           A PG  L+G+DSHTP  GG+G + +G GG      MAG P+ +  P+V+ V+L G L+GW
Sbjct: 109 ALPGATLVGSDSHTPTAGGIGSLAMGAGGLSVALAMAGEPYFISMPRVVRVRLEGRLTGW 168

Query: 242 SSPKDVILKVAGILTVKGGTGAIVEYHGPGVDSISCTGMATICNMGAEIGATTSVFPYNH 301
           +S KDVIL + G+LTVKGG G + E+ GPGV ++S    A I NMGAE+GAT S+FP + 
Sbjct: 169 ASAKDVILHLLGLLTVKGGVGKVFEFAGPGVATLSVPERAVITNMGAELGATASLFPSDE 228

Query: 302 RMKKYLSKTGREDIANLADEFKDHLVPDPGCHYDQLIEINLSELKPHINGPFTPDLAHPV 361
           R + +L+   RE       ++K  L  D    YD  I I+LS L P +  P  PD   PV
Sbjct: 229 RTRAFLASMDRE------GDWKP-LAADADATYDDEIVIDLSALVPLVAQPHMPDRVVPV 281

Query: 362 AEVGKVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVAKQALAHGLKCKSQFTITPGSE 421
           AE+          L +    IGSCTNSSY DM   A V +  + H     +   ++PGS+
Sbjct: 282 AELA--------GLSVDQVAIGSCTNSSYADMRMVAEVLRGRMVH---VGTDTMVSPGSK 330

Query: 422 QIRATIERDGYAQILRDLGGIVLANACGPCIGQWDRKDIKKGEKNTIVTSYNRNFTGRND 481
           Q+   +  +G  + L D G  +L  +CGPCIG      +  G     V ++NRNF GR+ 
Sbjct: 331 QVLKMLAAEGLVEPLLDAGVRILECSCGPCIGM-GGSPVSGG---VSVRTFNRNFEGRS- 385

Query: 482 ANPETHAFVTSPEIVTALAIAGTLKFNPETDYLTGTDGKKFRLEAPDADELPKGEFDPGQ 541
              +   ++ SP      A+ G  +F     + T     +   +AP    L         
Sbjct: 386 GTKDAKVYLVSPLTAAMAALHG--QFTDPATWGTPPAQPELPAKAPSIRHL--------- 434

Query: 542 DTYQHPPKDSSGQHVDVSPTSQRLQLLEPFDKWDGKDLEDLQILIKVKGKCTTDHISAAG 601
             +  PP+D SG  V   P    L+   P D     D     ++IK+    TTDHI  AG
Sbjct: 435 --FAFPPRDGSGVEVLRGPNIVALEQFTPMD-----DTVAAPVVIKLGDDITTDHIMPAG 487

Query: 602 PWLKFRGHLDNISNNLLIGAINIENGKANSVRNAVTQEFGPV-PDTARYYKKHGIRWVVI 660
                   + ++ +N+   A ++               FG V  D     +  GI  +V 
Sbjct: 488 ------AEITSLRSNVPAIAQHV---------------FGRVDADFVARARAAGIGVIVA 526

Query: 661 GDENYGEGSSREHAALEPRHLGGRAIITKSFARIHETNLKKQGLLPLTFADPADYNKIHP 720
           GD NYG+GSSREHAAL PRHLG RA+I +S ARIH  NL   G+LPL   D  DY+K+  
Sbjct: 527 GD-NYGQGSSREHAALAPRHLGIRAVIVRSLARIHRANLVNFGILPLILCDRTDYDKLAV 585

Query: 721 VDKLTIQGLKDFTPGKPLKCIIKHPNGTQETILLNHTFNETQIEWFRAGSALNRMK 776
              + I      T G  +   ++        I + +   + +++  RAG  LN ++
Sbjct: 586 GGTVAIPA-SAITAGGEVDVQVEGVG----AIRVRNDLTQKELDIIRAGGLLNHVR 636


Lambda     K      H
   0.317    0.136    0.412 

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: 1167
Number of extensions: 62
Number of successful extensions: 9
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: 780
Length of database: 641
Length adjustment: 39
Effective length of query: 741
Effective length of database: 602
Effective search space:   446082
Effective search space used:   446082
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 (21.6 bits)
S2: 55 (25.8 bits)

Align candidate 8502313 DvMF_3021 (aconitate hydratase (RefSeq))
to HMM TIGR01342 (putative aconitate hydratase (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/TIGR01342.hmm
# target sequence database:        /tmp/gapView.17271.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01342  [M=655]
Accession:   TIGR01342
Description: acon_putative: putative aconitate hydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   1.9e-262  858.2   0.0   2.2e-262  858.0   0.0    1.0  1  lcl|FitnessBrowser__Miya:8502313  DvMF_3021 aconitate hydratase (R


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Miya:8502313  DvMF_3021 aconitate hydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  858.0   0.0  2.2e-262  2.2e-262       2     646 ..       5     636 ..       4     641 .] 0.97

  Alignments for each domain:
  == domain 1  score: 858.0 bits;  conditional E-value: 2.2e-262
                         TIGR01342   2 laekilddhlvegdlepgeeiaikidqtlsqdatgtmvylefealevdevktelavsyidhqtlqtdfknaddhkyl 78 
                                       l++ki+  hlv+g++ pg ei+++idqtl+qdatgtm yl+fea++vd v+t+l+vsy+dh+tlq+ f+n ddh++l
  lcl|FitnessBrowser__Miya:8502313   5 LTQKIIAAHLVSGEMAPGAEIGLRIDQTLTQDATGTMAYLQFEAMGVDRVRTDLSVSYVDHNTLQMGFRNPDDHRFL 81 
                                       799************************************************************************** PP

                         TIGR01342  79 rsvakkygiylskpgngichqvhkerfakpgktllgsdshtptagglgqlaigaggldvavamageayylkmpkvvn 155
                                       r+va k+g+ +s pg gichq+h+e+fa pg tl+gsdshtptagg+g la+gaggl va amage+y++ mp+vv 
  lcl|FitnessBrowser__Miya:8502313  82 RTVAAKHGVIFSPPGTGICHQLHLENFALPGATLVGSDSHTPTAGGIGSLAMGAGGLSVALAMAGEPYFISMPRVVR 158
                                       ***************************************************************************** PP

                         TIGR01342 156 vrlkgklpewvtakdvilellrrlsvkgglgkvleytgegvkelsvperatitnmgaelgatssifpsdeitedyla 232
                                       vrl+g+l  w++akdvil ll  l+vkgg+gkv+e+ g+gv  lsvpera itnmgaelgat+s+fpsde+t+++la
  lcl|FitnessBrowser__Miya:8502313 159 VRLEGRLTGWASAKDVILHLLGLLTVKGGVGKVFEFAGPGVATLSVPERAVITNMGAELGATASLFPSDERTRAFLA 235
                                       ***************************************************************************** PP

                         TIGR01342 233 afdreeefvelladadaeydevivvdlselepliaepsspdnvvpvrevegikveqvvvgsctnsayvdllraakll 309
                                       ++dre ++  l adada yd++iv+dls l pl+a+p++pd vvpv e++g  v+qv +gsctns+y d+   a +l
  lcl|FitnessBrowser__Miya:8502313 236 SMDREGDWKPLAADADATYDDEIVIDLSALVPLVAQPHMPDRVVPVAELAGLSVDQVAIGSCTNSSYADMRMVAEVL 312
                                       ***************************************************************************** PP

                         TIGR01342 310 egrevskdvvlivapgskqalellaregallellkagvrileaacgacigigfvpasdsvslrsfnrnfkgragied 386
                                        gr v+  +  +v+pgskq l++la eg +  ll agvrile++cg+cig+g  p s +vs+r+fnrnf+gr+g++d
  lcl|FitnessBrowser__Miya:8502313 313 RGRMVHVGTDTMVSPGSKQVLKMLAAEGLVEPLLDAGVRILECSCGPCIGMGGSPVSGGVSVRTFNRNFEGRSGTKD 389
                                       ***************************************************************************** PP

                         TIGR01342 387 dkvylaspevavaaaiageivdprdlaedeglkairvemgekysygdeadidiltkeeridvelikgpnikslpvke 463
                                       +kvyl+sp +a+ aa+ g+  dp       g    + e++ k +   +     +++ +   ve+++gpni +l ++ 
  lcl|FitnessBrowser__Miya:8502313 390 AKVYLVSPLTAAMAALHGQFTDPAT----WGTPPAQPELPAKAPSIRHL--FAFPPRDGSGVEVLRGPNIVALEQFT 460
                                       ***********************76....57788899****99987655..578999******************** PP

                         TIGR01342 464 plgedvegevllkvednittdhiipatadilklrsniealseyvlsrvddefverakkldekgkagvlvagenygqg 540
                                       p+ ++v   v++k+ d+ittdhi+pa+a+i  lrsn+ a++++v+ rvd +fv ra+++      gv+vag+nygqg
  lcl|FitnessBrowser__Miya:8502313 461 PMDDTVAAPVVIKLGDDITTDHIMPAGAEITSLRSNVPAIAQHVFGRVDADFVARARAAGI----GVIVAGDNYGQG 533
                                       *********************************************************9988....************ PP

                         TIGR01342 541 ssrehaalaprflgveavlaksfarihkanlvnfgvlpleidnkedydkielgdevevvdliealkdgeeilvvrkt 617
                                       ssrehaalapr lg++av+ +s+arih+anlvnfg+lpl + ++ dydk+  g  v ++   +a++ g e + v+++
  lcl|FitnessBrowser__Miya:8502313 534 SSREHAALAPRHLGIRAVIVRSLARIHRANLVNFGILPLILCDRTDYDKLAVGGTVAIPA--SAITAGGE-VDVQVE 607
                                       **********************************************************95..56666655.567888 PP

                         TIGR01342 618 ddeeilatldlsevekeiliaggklslik 646
                                           i +  dl+++e +i+ agg l++++
  lcl|FitnessBrowser__Miya:8502313 608 GVGAIRVRNDLTQKELDIIRAGGLLNHVR 636
                                       88899999*****************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (655 nodes)
Target sequences:                          1  (641 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: 00:00:00.05
# Mc/sec: 7.26
//
[ok]

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

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Steps (tab-delimited)
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Protein sequences (fasta format)
Organisms (tab-delimited)
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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