Alignments for a candidate for acnD in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Stenotrophomonas chelatiphaga DSM 21508

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_057687523.1 ABB28_RS16850 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_001431535.1:WP_057687523.1
          Length = 917

 Score =  706 bits (1822), Expect = 0.0
 Identities = 399/916 (43%), Positives = 551/916 (60%), Gaps = 69/916 (7%)

Query: 1   MSTVMNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCE------ 54
           MS   +T+ +  + G   DYF   +  +       + LPY+ ++L ENL+R  +      
Sbjct: 1   MSDSFSTRSQLDVGGKRYDYFSLPKLGQRFD---ISHLPYSMKILLENLLRHEDGGVTVG 57

Query: 55  PEMLTASLKQIIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNP 114
            + + A      +++ E++  + PARVV  D  G   +VDLA +RDA+   GG P Q+NP
Sbjct: 58  KDHIEAVATWDPKAEPEIEIAFMPARVVLQDFTGVPCVVDLAAMRDAVVKLGGSPEQINP 117

Query: 115 VVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNG 174
            +P++L++DHS+ V+  G   +A   N  IE +RN++R+ F+ W QKAF N  V+P   G
Sbjct: 118 QIPSELVIDHSVQVDVFG-KPEALDLNGKIEFQRNQERYGFLRWGQKAFDNFKVVPPNTG 176

Query: 175 IMHQINLERMSPVIHA--RNG--VAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVML 230
           I+HQ+NLE ++ V+ A  ++G  VA+PDT+ GTDSHT  ++ +GV+  GVGG+EAE+ ML
Sbjct: 177 IVHQVNLENLARVVMAVDKDGTQVAYPDTVFGTDSHTTMINGIGVLGWGVGGIEAEAAML 236

Query: 231 GRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLG 290
           G+ S M +P ++G +LTG+   G TATD+VL +T+ LR   VV  ++EFFGEG + L L 
Sbjct: 237 GQPSSMLIPQVVGFKLTGQMPEGATATDLVLTVTQMLRKHGVVGKFVEFFGEGLQHLPLA 296

Query: 291 DRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSD-DLKQA 349
           DRATI NM PE+GAT  +F ID ++L+YL L+GR  EQ+ LVE YAK  GLW D D   A
Sbjct: 297 DRATIGNMAPEYGATCGIFPIDHESLNYLRLSGRPEEQIALVEAYAKAQGLWHDADTAHA 356

Query: 350 VYPRTLHFDLSSVVRTIAGPSNPHARV--------------------------------- 376
            Y  TL  D+ +V  ++AGP  P  RV                                 
Sbjct: 357 QYSATLELDMGTVKPSLAGPKRPQDRVLLEDVQANYREALVGLTTNRDKKDVDVSTFVNE 416

Query: 377 ------PTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNAN 430
                    +LA      E++ +   + DGAV+IAAITSCTNTSNP  +I AGLLARNA 
Sbjct: 417 GGGTAVGNEQLAKGQADVELDGKAFRLKDGAVVIAAITSCTNTSNPAVMIGAGLLARNAA 476

Query: 431 AKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSGALDPVI 490
           A+GL R+PWVKTSL PGS+ V  YL +A +L ELE LGF +VG+ CTTC G SG L   +
Sbjct: 477 ARGLNRQPWVKTSLGPGSRVVTDYLSKAGVLTELEKLGFYVVGYGCTTCIGNSGPLPAEV 536

Query: 491 QQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGL 550
              +   DL  T+VLSGNRNF+GR+HP  K  +LASPPLVVAYAIAGT   D+  + LG 
Sbjct: 537 SAGIALGDLVVTSVLSGNRNFEGRVHPEVKMNYLASPPLVVAYAIAGTTDIDLTTEPLGT 596

Query: 551 DKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSP---LYDWR 607
             DG+PV L +IWPS+ EI  VIAA++ PE F++ Y  +F     +    SP   LY+W 
Sbjct: 597 GSDGQPVYLRDIWPSNKEIGDVIAATLGPEMFKQNYADVFKGDSRWNTIASPDGDLYEWD 656

Query: 608 PQSTYIRRPPYWEG---ALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664
             STYI+ PPY++G    +     + G R + + GD+ITTDH+SP+  I  +S AG +L 
Sbjct: 657 DGSTYIKNPPYFDGMTMQVGSIDDVHGARVMGLFGDSITTDHISPAGNIKKESPAGRFLQ 716

Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEM--AIVDGKVKQGSLARIEPEGIVT 722
           + G+   DFNSY + RG+     R TFAN ++KN M      G       +  EPE +  
Sbjct: 717 ERGVQPADFNSYGSRRGNDDVMVRGTFANIRIKNLMFGGEEGGNTLYYPASGGEPEKLA- 775

Query: 723 RMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVG 782
            +++A   Y     PL+++AG +YG GSSRDWAAKG  L GV+A++AE FERIHR+NLVG
Sbjct: 776 -IYDAAIKYKADGVPLVVLAGKEYGTGSSRDWAAKGTLLLGVKAVIAESFERIHRSNLVG 834

Query: 783 MGVLPLEFKAGENRATYGIDGTEVFDVIG---SIAPRADLTVIITRKNGERVEVPVTCRL 839
           MGVLPL+F+ GEN  + G+DG+EVFD+ G     + RA  TV   + +G  V    +  L
Sbjct: 835 MGVLPLQFRNGENAQSLGLDGSEVFDITGLKDGASKRA--TVAAKKADGTVVTFEASVML 892

Query: 840 DTAEEVSIYEAGGVLQ 855
            T +EV  +  GG+LQ
Sbjct: 893 LTPKEVEYFRHGGLLQ 908


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: 2067
Number of extensions: 104
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 867
Length of database: 917
Length adjustment: 43
Effective length of query: 824
Effective length of database: 874
Effective search space:   720176
Effective search space used:   720176
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 24 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