Alignments for a candidate for acnD in Acidovorax sp. GW101-3H11

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Acidovorax sp. GW101-3H11

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate Ac3H11_2323 2-methylcitrate dehydratase FeS dependent (EC 4.2.1.79)

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2323
          Length = 889

 Score = 1353 bits (3502), Expect = 0.0
 Identities = 677/867 (78%), Positives = 758/867 (87%), Gaps = 9/867 (1%)

Query: 4   VMNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLK 63
           +MNT +R+PLPGT LDYFD R A+E + PGA+A LPYT+RV AE++VRR +P  +   L+
Sbjct: 1   MMNTLFRRPLPGTDLDYFDARAAVETLQPGAWATLPYTARVHAESIVRRADPATVNDCLR 60

Query: 64  QIIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVD 123
           Q+IE K++ DFPW+PARVVCHDILGQTALVDLAGLRDAIA  GGDPAQVNPVVP QLIVD
Sbjct: 61  QLIERKRDRDFPWYPARVVCHDILGQTALVDLAGLRDAIAKGGGDPAQVNPVVPVQLIVD 120

Query: 124 HSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLER 183
           HSLAVE GGFD DAFAKNRAIEDRRNEDRFHFI WT+KAF N+DVIP GNGIMHQINLE+
Sbjct: 121 HSLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIEWTKKAFANVDVIPAGNGIMHQINLEK 180

Query: 184 MSPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIG 243
           MSPV+HA  GVA+PDT VGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRAS MRLP+++G
Sbjct: 181 MSPVVHADRGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASMMRLPEMVG 240

Query: 244 VELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFG 303
           VELTG+ Q GITATD+VLALTEFLR  KVV +YLEFFGEGA  LTLGDRATISNM PE+G
Sbjct: 241 VELTGQRQDGITATDVVLALTEFLRKAKVVGAYLEFFGEGAAKLTLGDRATISNMAPEYG 300

Query: 304 ATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVV 363
           ATAA+F ID+QTLDYL LTGREA QVKLVETYAKTAGLW+D L  AVY RTL FDLS+VV
Sbjct: 301 ATAALFCIDEQTLDYLRLTGREARQVKLVETYAKTAGLWADALAGAVYDRTLRFDLSTVV 360

Query: 364 RTIAGPSNPHARVPTSELAARGISGE---VENEPGLMPDGAVIIAAITSCTNTSNPRNVI 420
           R +AGPSNPHARV TS+LAARGI+G         G MPDGAV+IAAITSCTNTSNPRNVI
Sbjct: 361 RNLAGPSNPHARVATSDLAARGIAGPWALPSPGEGTMPDGAVVIAAITSCTNTSNPRNVI 420

Query: 421 AAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCN 480
           AA LLARNA+  GLTRKPWVKTSLAPGS+ V+LYL+EA LL +LE+LGFGIV FACTTCN
Sbjct: 421 AAALLARNAHRLGLTRKPWVKTSLAPGSRVVELYLKEAGLLTDLEALGFGIVAFACTTCN 480

Query: 481 GMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIR 540
           GMSGALDP IQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGT+R
Sbjct: 481 GMSGALDPAIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTVR 540

Query: 541 FDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKV 600
           FDIEKDVL +  DG+P+RL ++WPSD EIDAV+ A+VKP  +R VYEPMF +  D G +V
Sbjct: 541 FDIEKDVLAV-VDGQPIRLKDLWPSDEEIDAVVKAAVKPAHYRAVYEPMFAIRHDDGPRV 599

Query: 601 SPLYDWRPQSTYIRRPPYWE----GALAGE-RTLKGMRPLAVLGDNITTDHLSPSNAIMM 655
           SP YDWRPQSTYIRRPPYW+    GALA   RTL+GMRPLA+L DNITTDHLSPSNAI+ 
Sbjct: 600 SPQYDWRPQSTYIRRPPYWDTEGIGALAAHPRTLQGMRPLALLPDNITTDHLSPSNAILP 659

Query: 656 DSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARI 715
           DSAAGEYL +MGLPEEDFNSYATHRGDHLTA RATFANP+L NEMA+VDGKV++GSLAR+
Sbjct: 660 DSAAGEYLARMGLPEEDFNSYATHRGDHLTALRATFANPQLVNEMAVVDGKVQKGSLARV 719

Query: 716 EPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERI 775
           EPEG V RMWEAIETY+ R+QPLIIIAGADYGQGSSRDWAAKGVRLAGVE +VAEGFERI
Sbjct: 720 EPEGQVMRMWEAIETYLHRRQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVVVAEGFERI 779

Query: 776 HRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPV 835
           HRTNL+GMGVLPLEF+AG NR T  ++GTEV+ V G + P A +T+++ RK GE V+VP+
Sbjct: 780 HRTNLIGMGVLPLEFEAGVNRTTLQLEGTEVYGVEGDLKPGATVTLVVQRKLGEVVKVPM 839

Query: 836 TCRLDTAEEVSIYEAGGVLQRFAQDFL 862
            CRLDTAEEVS+YEAGGVLQRFAQDFL
Sbjct: 840 RCRLDTAEEVSVYEAGGVLQRFAQDFL 866


Lambda     K      H
   0.318    0.136    0.397 

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: 2271
Number of extensions: 94
Number of successful extensions: 4
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: 867
Length of database: 889
Length adjustment: 43
Effective length of query: 824
Effective length of database: 846
Effective search space:   697104
Effective search space used:   697104
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: 56 (26.2 bits)

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

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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