Alignments for a candidate for acn in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for acn in Halomonas desiderata SP1

Align 2-methylcitrate dehydratase (EC 4.2.1.79) (characterized)
to candidate WP_086511662.1 BZY95_RS20075 2-methylcitrate dehydratase

Query= BRENDA::P77243
         (483 letters)



>NCBI__GCF_002151265.1:WP_086511662.1
          Length = 494

 Score =  608 bits (1567), Expect = e-178
 Identities = 304/490 (62%), Positives = 383/490 (78%), Gaps = 16/490 (3%)

Query: 7   NIRPEFDREIVDIVDYVMNYEISSKVAYDTAHYCLLDTLGCGLEALEYPACKKLLGPIVP 66
           N+RP++D E+  I DYV++Y I+S+ A +TA +CL+DTLGCGL AL +P C K LGP+V 
Sbjct: 8   NVRPDYDPELQKIADYVLDYRIASEEALETARHCLVDTLGCGLLALRFPECIKHLGPLVE 67

Query: 67  GTVVPNGVRVPGTQFQLDPVQAAFNIGAMIRWLDFNDTWLAAEWGHPSDNLGGILATADW 126
           GTVVPNG RVPGT F+LDPV+AA++IG ++RWLD+NDTWLAAEWGHPSDNLG ILA AD 
Sbjct: 68  GTVVPNGARVPGTAFRLDPVKAAWDIGCIVRWLDYNDTWLAAEWGHPSDNLGAILAVADH 127

Query: 127 LSRNAVASGKAPLTMKQVLTAMIKAHEIQGCIALENSFNRVGLDHVLLVKVASTAVVAEM 186
           LS+  VA G+APLTM+ VL AMIKAHEIQG +ALENSFNRVGLDHV+LVKVASTAV A +
Sbjct: 128 LSQKRVAQGEAPLTMRDVLEAMIKAHEIQGVLALENSFNRVGLDHVVLVKVASTAVAAHL 187

Query: 187 LGLTREEILNAVSLAWVDGQSLRTYRHAPNTGTRKSWAAGDATSRAVRLALMAKTGEMGY 246
           +G +RE++L+A+S AWVDGQSLRTYRHAPN G+RKSWAAGDATSR VRLA +A  GEMG 
Sbjct: 188 MGASREQLLSALSHAWVDGQSLRTYRHAPNAGSRKSWAAGDATSRGVRLADIALRGEMGV 247

Query: 247 PSALTAPVWGFYDVSF-----------KGE-SFRFQRPYGSYVMENVLFKISFPAEFHSQ 294
           P  L+AP WGFYDV F           +GE  FRFQR +G+YVMEN+LFKI+FPAEFH+Q
Sbjct: 248 PGVLSAPQWGFYDVLFSKTNKDQAIKPEGERKFRFQREFGTYVMENILFKIAFPAEFHAQ 307

Query: 295 TAVEAAMTLYEQMQAAGKTAADIEKVTIRTHEACIRIIDKKGPLNNPADRDHCIQYMVAI 354
           TA EAA+ L+ Q++      A+I++V I THE+ IRII K+G L NPADRDHC+QYMVA+
Sbjct: 308 TACEAAVRLHPQVK---DRLAEIQRVVITTHESAIRIISKEGELANPADRDHCLQYMVAV 364

Query: 355 PLLFGRLTAADYEDNV-AQDKRIDALREKINCFEDPAFTADYHDPEKRAIANAITLEFTD 413
           PL+FG LTA  YED+   Q   ID LR+K+   E+P +T +Y   +KR+IANAI + F+D
Sbjct: 365 PLIFGDLTAEHYEDDFHRQHPLIDVLRDKMEVVEEPRYTQEYLAADKRSIANAIQVFFSD 424

Query: 414 GTRFEEVVVEYPIGHARRRQDGIPKLVDKFKINLARQFPTRQQQRILEVSLDRARLEQMP 473
           GT  E + VEYPIGH RRR +GIP L +KF+ +LA +FP  + +RI+ +  D+A+LE MP
Sbjct: 425 GTATECIEVEYPIGHRRRRDEGIPILEEKFRRHLATRFPAGRCERIIALCQDQAQLEAMP 484

Query: 474 VNEYLDLYVI 483
           V+ ++DL+VI
Sbjct: 485 VHRFVDLFVI 494


Lambda     K      H
   0.321    0.136    0.406 

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: 737
Number of extensions: 26
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: 483
Length of database: 494
Length adjustment: 34
Effective length of query: 449
Effective length of database: 460
Effective search space:   206540
Effective search space used:   206540
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 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