Alignments for a candidate for dopDH in Mycolicibacterium vanbaalenii PYR-1

GapMind for catabolism of small carbon sources

Alignments for a candidate for dopDH in Mycolicibacterium vanbaalenii PYR-1

Align α-ketoglutaric semialdehyde dehydrogenase subunit (EC 1.2.1.26) (characterized)
to candidate WP_011778304.1 MVAN_RS05210 aldehyde dehydrogenase (NADP(+))

Query= metacyc::G1G01-1343-MONOMER
         (525 letters)



>NCBI__GCF_000015305.1:WP_011778304.1
          Length = 532

 Score =  637 bits (1644), Expect = 0.0
 Identities = 335/520 (64%), Positives = 380/520 (73%), Gaps = 2/520 (0%)

Query: 3   LTGNLLIGQRPVTGSRDAIRAIDPTTGQTLEPAYLGGTGEHVAQACALAWAAFDAYRETS 62
           LTG +LI   PV G+   +RA DP  GQ LEP Y  G   HV  ACA A  AF  YR T+
Sbjct: 11  LTGQMLIAGAPVRGTGKEVRAFDPAAGQPLEPVYQHGDNTHVDAACAAAADAFAQYRATT 70

Query: 63  LEQRAEFLEAIATQIEALGDALIDRAVIETGLPKARIQGERGRTCTQLRTFARTVRAGEW 122
            EQRA FL+ IAT IEA+G+ALI RAV E+GLP+ARI GE GRT  QLR FA  +R G W
Sbjct: 71  SEQRAAFLDTIATNIEAVGEALIARAVAESGLPQARITGELGRTTGQLRLFASVLREGSW 130

Query: 123 LDVRIDSALPERQPLPRADLRQRQVALGPVAVFGASNFPLAFSVAGGDTASALAAGCPVV 182
              RID+ALP+R PLPR DLRQR + LGPVAVF ASNFPLAFSVAGGDTASALAAGCPVV
Sbjct: 131 NGARIDTALPDRTPLPRPDLRQRHIPLGPVAVFSASNFPLAFSVAGGDTASALAAGCPVV 190

Query: 183 VKAHSAHPGTSELVGQAVAQAVKQCGLPEGVFSLLYGSGREVGIALVSDPRIKAVGFTGS 242
           VK H AHPGTSELV +AV  AV   GLP G FSLL+GSG  +GIALV+DPRIKAVGFTGS
Sbjct: 191 VKGHDAHPGTSELVARAVTDAVTTSGLPAGTFSLLFGSGPGLGIALVTDPRIKAVGFTGS 250

Query: 243 RSGGMALCQAAQARPEPIPVYAEMSSINPVFLFDAALQARAEALAQGFVASLTQGAGQFC 302
           RSGGMAL  AA ARPEPIPVYAEMSSINPVF+ D AL+ R   L + FVASLT G+GQFC
Sbjct: 251 RSGGMALVSAAAARPEPIPVYAEMSSINPVFVLDGALKTRGAELGRAFVASLTMGSGQFC 310

Query: 303 TNPGLVIARQGPALQRFITAAAGYVQQGAAQTMLTPGIFSAYQAGIAALADNPHAQAITS 362
           TNPGLVIA  GP L  F  AA   +    A  MLTP I  +Y +G+ AL+    AQ +  
Sbjct: 311 TNPGLVIAVDGPGLDTFAAAARDALAGSPATPMLTPTIARSYASGVEALSG--AAQLVGR 368

Query: 363 GQAGQGPNQCQAQLFVTQAEAFLADPALQAEVFGAASLVVACTDDEQVRQVAEHLEGQLT 422
           G  G     C A LF T A+ FLA  ALQAEVFG++SL+V C D EQ+R VAE +EGQLT
Sbjct: 369 GAPGTSETACHAALFSTDAQTFLASEALQAEVFGSSSLIVRCADFEQMRAVAEGIEGQLT 428

Query: 423 ATLQLDEADIDSARALLPTLERKAGRILVNGWPTGVEVCDAMVHGGPFPATSDARTTSVG 482
           AT+  D++D+D A  LLP LE KAGRIL  GWPTGVEVC AMVHGGPFPATSD+R+TSVG
Sbjct: 429 ATVHADDSDLDDAGRLLPLLELKAGRILFGGWPTGVEVCHAMVHGGPFPATSDSRSTSVG 488

Query: 483 TAAILRFLRPVCYQDVPDALLPQALKHGNPLQLRRLLDGK 522
           + AI R+LRPVCYQDVP  LLP A+  GNP +L R +DG+
Sbjct: 489 SQAIERYLRPVCYQDVPAPLLPSAIAEGNPEKLWRRVDGR 528


Lambda     K      H
   0.319    0.134    0.391 

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: 927
Number of extensions: 31
Number of successful extensions: 2
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: 525
Length of database: 532
Length adjustment: 35
Effective length of query: 490
Effective length of database: 497
Effective search space:   243530
Effective search space used:   243530
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 (21.8 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