Alignments for a candidate for acn in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Desulfovibrio vulgaris Hildenborough

Align Aconitate hydratase, mitochondrial; Aconitase; Citrate hydro-lyase; EC 4.2.1.3 (characterized)
to candidate 206498 DVU1064 aconitate hydratase, putative

Query= SwissProt::P20004
         (780 letters)



>MicrobesOnline__882:206498
          Length = 642

 Score =  357 bits (915), Expect = e-102
 Identities = 256/718 (35%), Positives = 366/718 (50%), Gaps = 86/718 (11%)

Query: 62  PLTLSEKIVYGHLDDPANQEIERGKTYLRLRPDRVAMQDATAQMAMLQFISSGLPKVAVP 121
           PL  ++KI+  HL    + ++  G   + LR D+   QDAT  MA LQF + G+ +V   
Sbjct: 2   PLNQTQKIIKAHL---VHGDMAPGAP-IALRIDQTLTQDATGTMAYLQFEAMGVDRVRTD 57

Query: 122 STI-HCDHLIEAQLGGEKDLRRAKDINQEVYNFLATAGAKYGVGFWRPGSGIIHQIILEN 180
            ++ + DH    Q+G     R A D     + FL T  A++G+ F  PG+GI HQ+ LEN
Sbjct: 58  LSVSYVDHNT-LQMG----FRNADD-----HRFLRTVAARHGIVFSAPGNGICHQLHLEN 107

Query: 181 YAYPGVLLIGTDSHTPNGGGLGGICIGVGGADAVDVMAGIPWELKCPKVIGVKLTGSLSG 240
           +  PG  L+G+DSHTP  GG+G + +G GG      MAG P+ +  PKV+ V+L G L+G
Sbjct: 108 FGRPGATLVGSDSHTPTAGGIGALAMGAGGLSVALSMAGEPYTITMPKVVNVRLEGRLTG 167

Query: 241 WTSPKDVILKVAGILTVKGGTGAIVEYHGPGVDSISCTGMATICNMGAEIGATTSVFPYN 300
           W + KDVIL + G+LTVKGG G + EY GPGV ++S    ATI NMGAE+GATTS+FP +
Sbjct: 168 WAAAKDVILHLLGLLTVKGGVGRVFEYTGPGVATLSVPERATITNMGAELGATTSIFPSD 227

Query: 301 HRMKKYLSKTGR-ADIANLADEFKDHLVPDSGCHYDQLIEINLSELKPHINGPFTPDLAH 359
              + +L+  GR AD   LA         D+G  YD+ + I+LS+L+P +  P  PD   
Sbjct: 228 ESTRAFLAAMGREADWQPLA--------ADAGAVYDEEVVIDLSQLEPLVATPHMPDRVV 279

Query: 360 PVAEVGSVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVAKQALAHGLQCKSQFTITPG 419
            VA +          L +    IGSCTNSSY D+    +VA+      +   +   I+PG
Sbjct: 280 TVASLAG--------LKVDQVAIGSCTNSSYADL---KSVAQVVAGRRVDSTTDCMISPG 328

Query: 420 SEQIRATIERDGYAQILRDVGGIVLANACGPCIGQWDRKDIKKGEKNTIVTSYNRNFTGR 479
           S+Q+   +  +G  + L D G  +L   CGPCIG      +  G     V ++NRNF GR
Sbjct: 329 SKQVLRMLATEGLLEPLLDAGIRMLECTCGPCIGM-GGSPVSGG---VSVRTFNRNFEGR 384

Query: 480 NDANPETHAFVTSPEIVTALAIAGTLKFNPETDFLTGKDGKKFKLEAPDADELPRAEFDP 539
           +    +   ++ SP     +A+ G       TD  T         EAP   ELP A+   
Sbjct: 385 S-GTKDAGVYLASPLTAAMVALHGGF-----TDPATWG-------EAPAVPELP-ADVPS 430

Query: 540 GQDTYQHPPKDSSGQQVDVSPTSQRLQLLEPFDKWDGRDLEDLQILIKVKGKCTTDHISA 599
            +  +  PP+D S  +V   P    LQ  E        D  D +++I++    TTDHI  
Sbjct: 431 IRHLFVFPPEDGSQVEVQRGPNIVALQTFEGLP-----DRLDAEVVIRLGDDITTDHIMP 485

Query: 600 AGPWL-KFRGHLDNISNNLLIGAINVENGKANSVRNAVTQEFGPVPDTARYYKKHGIRWV 658
           AG  +   R ++  IS + + G ++     A+ V+ A     G                V
Sbjct: 486 AGAEITALRSNVPAISRH-VFGRVD-----ADFVKRAEAAANG----------------V 523

Query: 659 VIGDENYGEGSSREHAALEPRHLGGRAIITKSFARIHETNLKKQGLLPLTFADPADYNKI 718
           ++  ENYG+GSSREHAAL PRHLG RA+I KS ARIH  NL   G+LPL   D  DY ++
Sbjct: 524 IVAGENYGQGSSREHAALAPRHLGIRAVIAKSLARIHRANLVNFGILPLILVDKGDYERL 583

Query: 719 HPVDKLTIKGLKDFAPGKPLTCIIKHPNGTQETILLNHTFNETQIEWFRAGSALNRMK 776
                +TI      A G+   C +   +G    +  + T +E +I   RAG  LN ++
Sbjct: 584 EQGGNVTIPVADIIAGGE---CAVALADGGSVRVRNDLTVDELEI--IRAGGLLNYVR 636


Lambda     K      H
   0.317    0.136    0.411 

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: 1154
Number of extensions: 70
Number of successful extensions: 8
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: 642
Length adjustment: 39
Effective length of query: 741
Effective length of database: 603
Effective search space:   446823
Effective search space used:   446823
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 206498 DVU1064 (aconitate hydratase, putative)
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.12880.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                       -----------
   4.7e-268  876.7   0.1   5.4e-268  876.5   0.1    1.0  1  lcl|MicrobesOnline__882:206498  DVU1064 aconitate hydratase, put


Domain annotation for each sequence (and alignments):
>> lcl|MicrobesOnline__882:206498  DVU1064 aconitate hydratase, putative
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  876.5   0.1  5.4e-268  5.4e-268       3     649 ..       6     639 ..       4     642 .] 0.97

  Alignments for each domain:
  == domain 1  score: 876.5 bits;  conditional E-value: 5.4e-268
                       TIGR01342   3 aekilddhlvegdlepgeeiaikidqtlsqdatgtmvylefealevdevktelavsyidhqtlqtdfknaddhkylrsv 81 
                                     ++ki++ hlv+gd+ pg  ia++idqtl+qdatgtm yl+fea++vd v+t+l+vsy+dh+tlq+ f+naddh++lr+v
  lcl|MicrobesOnline__882:206498   6 TQKIIKAHLVHGDMAPGAPIALRIDQTLTQDATGTMAYLQFEAMGVDRVRTDLSVSYVDHNTLQMGFRNADDHRFLRTV 84 
                                     79***************************************************************************** PP

                       TIGR01342  82 akkygiylskpgngichqvhkerfakpgktllgsdshtptagglgqlaigaggldvavamageayylkmpkvvnvrlkg 160
                                     a ++gi +s pgngichq+h+e+f +pg tl+gsdshtptagg+g la+gaggl va +mage+y + mpkvvnvrl+g
  lcl|MicrobesOnline__882:206498  85 AARHGIVFSAPGNGICHQLHLENFGRPGATLVGSDSHTPTAGGIGALAMGAGGLSVALSMAGEPYTITMPKVVNVRLEG 163
                                     ******************************************************************************* PP

                       TIGR01342 161 klpewvtakdvilellrrlsvkgglgkvleytgegvkelsvperatitnmgaelgatssifpsdeitedylaafdreee 239
                                     +l  w++akdvil ll  l+vkgg+g+v+eytg+gv  lsvperatitnmgaelgat+sifpsde t+++laa++re +
  lcl|MicrobesOnline__882:206498 164 RLTGWAAAKDVILHLLGLLTVKGGVGRVFEYTGPGVATLSVPERATITNMGAELGATTSIFPSDESTRAFLAAMGREAD 242
                                     ******************************************************************************* PP

                       TIGR01342 240 fvelladadaeydevivvdlselepliaepsspdnvvpvrevegikveqvvvgsctnsayvdllraakllegrevskdv 318
                                     +  l ada a yde++v+dls+lepl+a p++pd vv v  ++g kv+qv +gsctns+y dl   a+++ gr+v+  +
  lcl|MicrobesOnline__882:206498 243 WQPLAADAGAVYDEEVVIDLSQLEPLVATPHMPDRVVTVASLAGLKVDQVAIGSCTNSSYADLKSVAQVVAGRRVDSTT 321
                                     ******************************************************************************* PP

                       TIGR01342 319 vlivapgskqalellaregallellkagvrileaacgacigigfvpasdsvslrsfnrnfkgragieddkvylaspeva 397
                                       +++pgskq l +la eg l  ll ag+r+le++cg+cig+g  p s +vs+r+fnrnf+gr+g++d+ vylasp +a
  lcl|MicrobesOnline__882:206498 322 DCMISPGSKQVLRMLATEGLLEPLLDAGIRMLECTCGPCIGMGGSPVSGGVSVRTFNRNFEGRSGTKDAGVYLASPLTA 400
                                     ******************************************************************************* PP

                       TIGR01342 398 vaaaiageivdprdlaedeglkairvemgekysygdeadidiltkeeridvelikgpnikslpvkeplgedvegevllk 476
                                     +  a+ g   dp    e   +     e++ + +   +  + ++++e+  +ve+ +gpni +l  +e l++ ++ ev+++
  lcl|MicrobesOnline__882:206498 401 AMVALHGGFTDPATWGEAPAVP----ELPADVPSIRH--LFVFPPEDGSQVEVQRGPNIVALQTFEGLPDRLDAEVVIR 473
                                     *************999887765....77777776555..55799*********************************** PP

                       TIGR01342 477 vednittdhiipatadilklrsniealseyvlsrvddefverakkldekgkagvlvagenygqgssrehaalaprflgv 555
                                     + d+ittdhi+pa+a+i  lrsn+ a+s +v+ rvd +fv+ra ++ +    gv+vagenygqgssrehaalapr lg+
  lcl|MicrobesOnline__882:206498 474 LGDDITTDHIMPAGAEITALRSNVPAISRHVFGRVDADFVKRAEAAAN----GVIVAGENYGQGSSREHAALAPRHLGI 548
                                     *********************************************999....*************************** PP

                       TIGR01342 556 eavlaksfarihkanlvnfgvlpleidnkedydkielgdevevvdliealkdgeeilvvrktddeeilatldlseveke 634
                                     +av+aks+arih+anlvnfg+lpl + +k dy+++e+g +v ++ +++ ++ ge   +v  +d+  + +  dl+  e e
  lcl|MicrobesOnline__882:206498 549 RAVIAKSLARIHRANLVNFGILPLILVDKGDYERLEQGGNVTIP-VADIIAGGE--CAVALADGGSVRVRNDLTVDELE 624
                                     ******************************************98.788888876..5677899999************* PP

                       TIGR01342 635 iliaggklslikqkh 649
                                     i+ agg l+++++  
  lcl|MicrobesOnline__882:206498 625 IIRAGGLLNYVRNAR 639
                                     ***********9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (655 nodes)
Target sequences:                          1  (642 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 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 12.40
//
[ok]

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

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Protein sequences (fasta format)
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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