Alignments for a candidate for acnD in Pseudoalteromonas arctica A 37-1-2

GapMind for catabolism of small carbon sources

Alignments for a candidate for acnD in Pseudoalteromonas arctica A 37-1-2

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate WP_010554785.1 PARC_RS00780 aconitate hydratase AcnA

Query= BRENDA::Q8EJW3
         (867 letters)



>NCBI__GCF_000238395.3:WP_010554785.1
          Length = 914

 Score =  700 bits (1806), Expect = 0.0
 Identities = 386/888 (43%), Positives = 542/888 (61%), Gaps = 66/888 (7%)

Query: 37  KLPYTSRVLAENLVRR-----CEPEMLTASLKQIIESKQELDFPWFPARVVCHDILGQTA 91
           +LP++ +VL ENL+R       + + + A L    ++K   +  + PARVV  D  G  A
Sbjct: 32  RLPFSLKVLLENLLRNEDGANIKEQDIQALLNWDPQAKPASEVAFTPARVVMQDFTGVPA 91

Query: 92  LVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNED 151
           +VDLA +RDA+   GGDPA++NP+ P +L++DHS+ V+  G D  AF  N  +E  RN++
Sbjct: 92  IVDLAAMRDAMEKLGGDPAKINPLSPAELVIDHSVQVDGYGND-GAFDLNAKLEYDRNKE 150

Query: 152 RFHFINWTQKAFKNIDVIPQGNGIMHQINLERMSPVI--HARNG--VAFPDTLVGTDSHT 207
           R+ F+ W Q AF N+ V+P   GI+HQ+NLE ++ V+    R+G   A+PDTLVGTDSHT
Sbjct: 151 RYEFLRWGQTAFDNLKVVPPATGIVHQVNLEYLARVVFNEERDGKKFAYPDTLVGTDSHT 210

Query: 208 PHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGVELTGKPQPGITATDIVLALTEFL 267
             ++ LGV+  GVGG+EAE+ MLG+   + +P ++G++L+G+   G TATD+VL +TE L
Sbjct: 211 TMINGLGVLGWGVGGIEAEAAMLGQPISLLIPQVVGMKLSGRLPEGTTATDLVLTVTEIL 270

Query: 268 RAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTLTGREAE 327
           R   VV  ++EF+G+G   L L DRATI+NM PE+GAT  +F ID +T++YL LT R+  
Sbjct: 271 RNHGVVGKFVEFYGDGLADLPLADRATIANMAPEYGATCGIFPIDDETINYLRLTNRDES 330

Query: 328 QVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARVPTSE------- 380
            +K++E YAK  GLW +D  +A Y  TL   L  VV ++AGP  P  R+   +       
Sbjct: 331 HLKVIEDYAKHQGLWRNDGDEASYTDTLELKLGDVVPSLAGPKRPQDRISLDKAGEVISQ 390

Query: 381 ---------LAARGISGE----VENE-PGLMPD-------------------------GA 401
                    +A R  S E    +E+E P   PD                         GA
Sbjct: 391 HLKNFQDERMARRDNSDEEQARIESEGPTTNPDEPVNEAQFMGAAKVKFKGQEFELNDGA 450

Query: 402 VIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLL 461
            +IAAITSCTNTSNP  ++AAGL+A+ A   G+  KPWVKTSLAPGSK V  YLE+A L+
Sbjct: 451 CVIAAITSCTNTSNPSVILAAGLVAKKAKQLGINVKPWVKTSLAPGSKVVTDYLEKAGLM 510

Query: 462 PELESLGFGIVGFACTTCNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQ 521
            +LESLGF +VG+ CTTC G SG L   I   +    L  +++LSGNRNF+GRIH   K 
Sbjct: 511 DDLESLGFNLVGYGCTTCIGNSGPLATEISDAIQKHKLVVSSILSGNRNFEGRIHQDVKM 570

Query: 522 AFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQ 581
            FLASPPLVVAYAIAG    D+  + L  D +G  + L NIWPS  E+  ++  +V  E 
Sbjct: 571 NFLASPPLVVAYAIAGRTDIDVYNEPLAQDANGNDIYLKNIWPSVKEVSDLVKETVTKEM 630

Query: 582 FRKVYEPMFDLSVDYGDKVSP---LYDWRPQSTYIRRPPYWEGALA---GERTLKGMRPL 635
           F K Y  +++    +     P   LYDW   STYI++ P+++G      G  T++G R L
Sbjct: 631 FEKSYANVYEGDSRWQQIKIPDGKLYDWDDASTYIKKAPFFDGMKVEPPGIPTIEGARCL 690

Query: 636 AVLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPK 695
           A LGD++TTDH+SP+ AI  D+ AG YL + G+ +  FNSY + RG+H    R TFAN +
Sbjct: 691 AKLGDSVTTDHISPAGAIKADAPAGLYLQENGVDKAQFNSYGSRRGNHEVMMRGTFANVR 750

Query: 696 LKNEMAIVDGKVKQGSLARIEPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWA 755
           LKN +A       +G + R +P   +  +++A   Y     PLII+AG +YG GSSRDWA
Sbjct: 751 LKNLLA----PGTEGGVTRTQPGDTLESIYDAAMEYQKNNTPLIILAGKEYGTGSSRDWA 806

Query: 756 AKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAP 815
           AKG  L GV+A+VA+ +ERIHR+NL+GMGVLPL+FK GE+  ++G+ G E FD+ G    
Sbjct: 807 AKGSLLLGVKAVVAQSYERIHRSNLIGMGVLPLQFKEGESYESHGLTGQEQFDIDGLYDK 866

Query: 816 RADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 863
             ++TVI T   G++V +    R+DT +E   Y+ GG+LQ   ++ L+
Sbjct: 867 TDEVTVIATNAEGKKVTLSADVRIDTPKEWDYYKHGGILQYVLRNMLD 914


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: 1954
Number of extensions: 91
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: 914
Length adjustment: 43
Effective length of query: 824
Effective length of database: 871
Effective search space:   717704
Effective search space used:   717704
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