Alignments for a candidate for acn in Pedobacter sp. GW460-11-11-14-LB5

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Pedobacter sp. GW460-11-11-14-LB5

Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate CA265_RS16400 CA265_RS16400 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase

Query= BRENDA::P36683
         (865 letters)



>FitnessBrowser__Pedo557:CA265_RS16400
          Length = 921

 Score =  323 bits (829), Expect = 2e-92
 Identities = 288/929 (31%), Positives = 446/929 (48%), Gaps = 118/929 (12%)

Query: 4   EYRKHVAERAAEGIAPKPLD-ANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEAAY 62
           +Y + + +R A+G+ PKP+D A  ++ ++  +KN      E  ++       PG   AA 
Sbjct: 6   DYIQEIEDRKAQGLHPKPIDGAELLSEIITQIKNVNNINREEAVNFFIYNTLPGTTAAAA 65

Query: 63  VKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDAL--DDAKLAPIAAKALS 120
           VKA FL  I   E     +TP+ A ELL  M+GG +I  L+D    D+   A  AA  L 
Sbjct: 66  VKAQFLKEIILAEVIVAEITPDFAFELLSHMKGGPSIKVLLDIALADNGDKAKKAADVLK 125

Query: 121 HTLLMFDNFYD-VEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKV-TGETN 178
             + ++D   D +++    GNE AK++++S+A AE+F   P +AE++ V  F    G+ +
Sbjct: 126 TQVYLYDADTDRLKDAYNNGNEIAKEILESYAKAEFFTKLPEVAEEIKVVTFIAGIGDIS 185

Query: 179 TDDLSPAPDAWSRPDIPLHALAMLK-NAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVG 237
           TD LSP   A SR D  LH   M+   A+E I+  Q     P K +  + +KG       
Sbjct: 186 TDLLSPGNQAHSRSDRELHGKCMITPEAQEEIKALQ--AQHPDKSVMLVAEKG------- 236

Query: 238 DVVGTGSSRKSATNSV-LWFMGDDIPHVPNKRGGGLCLGGK-IAPIFFNTMEDAGALPIE 295
             +G GSSR S  N+V LW      P+VP      +  G   I+PIF  T++  G + I+
Sbjct: 237 -TMGVGSSRMSGVNNVALWTGKRSSPYVPFVNIAPIVGGTNGISPIFLTTVDVTGGIGID 295

Query: 296 VD------------VSN------------LNMGDVIDVYPYKGEVRNHETGELLATFELK 331
           +             + N            +  G V+ +     ++ N E  EL+   +  
Sbjct: 296 LQNWVKKTDENGNVIRNEKDEPILEQRFSVETGTVLTINTKTKKLYNGEQ-ELIDISKAL 354

Query: 332 TDVLIDEVRAGGRIPLIIGRGLTTKAREALGLPHSDVFRQAKDVAESDRGFSLAQKMVGR 391
           T   ++ ++AGG   +I G+ + T A + LG+  S VF  AK+V+   +G +  +K+  R
Sbjct: 355 TPQKMEFMKAGGSYAIIFGKKIQTFAAKTLGIEASSVFAPAKEVSYEGQGLTAVEKIFNR 414

Query: 392 -ACGV---KGIRPGAYCEPKMTSVGSQDTTGPMTRDELKDLACLGFS--ADLVMQSFCHT 445
            A G+   K +  G+    ++  VGSQDTTG MT  EL+ +A    S   D   QS CHT
Sbjct: 415 NAVGLTQGKVLHAGSDVRVEVNIVGSQDTTGLMTAQELEAMAATVISPIVDGAYQSGCHT 474

Query: 446 AA-YPKPVDVNTHHTLPDFIMNRGGVSLRPGDG-------VIHSWLNRMLLPD-TVGTGG 496
           A+ + K    N    L  F+ + G ++ R   G       VIH  LN + + +  +  GG
Sbjct: 475 ASVWDKKAQANIPK-LMKFMNDFGVITARDPKGEYHSMTDVIHKVLNDITIDEWAIIIGG 533

Query: 497 DSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGITLRDLVHAIPLY 556
           DSHTR   G++F A SG VA A ATG   + +PESV V FKG M+  +  RD+VHA  L 
Sbjct: 534 DSHTRMSKGVAFGADSGTVALALATGEASMPIPESVKVTFKGLMKEHMDFRDVVHATQLQ 593

Query: 557 AIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASAERSAAGCTIKLNKEPI 616
            ++Q          +N+F GRI+E+  +  L  +QAF  TD +AE  A         + +
Sbjct: 594 MLQQ-------FDGENVFQGRIIEVH-IGTLLADQAFTFTDWTAEMKAKASICISQDDTL 645

Query: 617 IEYLNSNIVLLKWMIAEGYGDRRTL--------ERRIQGMEKWLANPELLEADADAEYAA 668
           I+ L      ++ MI +G  +   +         +RI+ ++  +  P L+  D +A+Y A
Sbjct: 646 IQSLEIAKNRIQIMIDKGMDNHNQVLQGLINKANKRIEEIKTGI-KPALM-PDDNAKYYA 703

Query: 669 VIDIDLADIKEPILCAPN----------DPDDARPLSAVQGE-KIDEVFIGSCMTNIGHF 717
            + IDL  I+EP++  P+            D  R L+   G+ K+D  F+GSCM +    
Sbjct: 704 EVVIDLDLIEEPMIADPDVNNADVSKRYTHDTIRDLTFYGGDKKVDLGFVGSCMVHKDDL 763

Query: 718 RAAGKLL-----DAHKGQLPTRLWVAPPTRMDAAQLTEEG------------YYSVFGKS 760
           +   ++L        K +    L VA PT     +L  EG            +     KS
Sbjct: 764 KIVSQMLKNVETQTGKVEFKAPLVVAAPTYNIIDELKAEGDWEYLQKYSGFEFSDALPKS 823

Query: 761 GAR--------IEIPGCSLCMGNQARVADGATVVSTSTRNFPNRL-----GTGANVFLAS 807
            AR        +E PGC+LCMGNQ + A G TV++TSTR F  R+     G      LAS
Sbjct: 824 AARTEYENIMYLERPGCNLCMGNQEKAAKGDTVMATSTRLFQGRVVEDKDGKKGESLLAS 883

Query: 808 AELAAVAALIGKLPTPEEYQTYVAQVDKT 836
             +  ++A++G++P+ EEY+  V  ++ T
Sbjct: 884 TPVVVLSAILGRIPSIEEYKVAVEGINLT 912


Lambda     K      H
   0.317    0.136    0.400 

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: 1666
Number of extensions: 82
Number of successful extensions: 14
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: 865
Length of database: 921
Length adjustment: 43
Effective length of query: 822
Effective length of database: 878
Effective search space:   721716
Effective search space used:   721716
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