Alignments for a candidate for dopDH in Collimonas pratensis Ter91

GapMind for catabolism of small carbon sources

Alignments for a candidate for dopDH in Collimonas pratensis Ter91

Align α-ketoglutaric semialdehyde dehydrogenase subunit (EC 1.2.1.26) (characterized)
to candidate WP_061935892.1 CPter91_RS01190 aldehyde dehydrogenase (NADP(+))

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



>NCBI__GCF_001584185.1:WP_061935892.1
          Length = 525

 Score =  626 bits (1615), Expect = 0.0
 Identities = 330/521 (63%), Positives = 388/521 (74%), Gaps = 1/521 (0%)

Query: 1   MPLTGNLLIGQRPVTGSRDAIRAIDPTTGQTLEPAYLGGTGEHVAQACALAWAAFDAYRE 60
           M +TG +LIGQ  V G+  ++RA++P T +T+ P +  G+   V QAC LA  AFD YRE
Sbjct: 1   MNITGEMLIGQTAVRGTEGSVRAVNPATNETIAPDFGAGSTAAVEQACKLAQQAFDTYRE 60

Query: 61  TSLEQRAEFLEAIATQIEALGDALIDRAVIETGLPKARIQGERGRTCTQLRTFARTVRAG 120
           T+ EQRA+FLE IAT I  LG  LI+RA  E+GLP AR++GERGRT  QLR FA+ +R G
Sbjct: 61  TTPEQRAQFLEEIATGILNLGPQLIERASQESGLPAARLEGERGRTVGQLRLFAKVIRDG 120

Query: 121 EWLDVRIDSALPERQPLPRADLRQRQVALGPVAVFGASNFPLAFSVAGGDTASALAAGCP 180
            +L   +DSALPER P PRADLR R++A+GPVAVFGASNFPLAFSVAGGDTA+ALAAGCP
Sbjct: 121 HYLSATLDSALPERTP-PRADLRLRKIAIGPVAVFGASNFPLAFSVAGGDTAAALAAGCP 179

Query: 181 VVVKAHSAHPGTSELVGQAVAQAVKQCGLPEGVFSLLYGSGREVGIALVSDPRIKAVGFT 240
           VVVK H+AHPGTSELVG+ + QAV  C LP GVFSL+ GSG EVG ALVS P IKAVGFT
Sbjct: 180 VVVKTHNAHPGTSELVGRVIQQAVAACQLPAGVFSLIIGSGNEVGQALVSHPAIKAVGFT 239

Query: 241 GSRSGGMALCQAAQARPEPIPVYAEMSSINPVFLFDAALQARAEALAQGFVASLTQGAGQ 300
           GSR GG+AL +AA  R EPIPVYAEMSSINP+FL   AL ARA  +   F  SLT G GQ
Sbjct: 240 GSRQGGLALMRAAAQRREPIPVYAEMSSINPMFLLPNALAARATQIGSAFADSLTMGVGQ 299

Query: 301 FCTNPGLVIARQGPALQRFITAAAGYVQQGAAQTMLTPGIFSAYQAGIAALADNPHAQAI 360
           FCTNPGLVI      L +F  AA+  ++  AA TMLTPGI SAY AG+  +       A+
Sbjct: 300 FCTNPGLVIGLASEHLAQFQEAASNALKAKAAGTMLTPGIHSAYLAGVERMQAVSGVDAV 359

Query: 361 TSGQAGQGPNQCQAQLFVTQAEAFLADPALQAEVFGAASLVVACTDDEQVRQVAEHLEGQ 420
             G A   P   QA LF T A  FLA   L+ E+FG +SL+VAC D++++R VAEHL GQ
Sbjct: 360 GRGMAASAPCAAQAALFATDAATFLASEQLEDEIFGPSSLIVACKDEDEMRAVAEHLAGQ 419

Query: 421 LTATLQLDEADIDSARALLPTLERKAGRILVNGWPTGVEVCDAMVHGGPFPATSDARTTS 480
           LTATLQL+ AD   A+ LLPTLERKAGRILVNG+PTGVEV  AMVHGGPFPATSD+R+TS
Sbjct: 420 LTATLQLEAADHALAKTLLPTLERKAGRILVNGFPTGVEVSYAMVHGGPFPATSDSRSTS 479

Query: 481 VGTAAILRFLRPVCYQDVPDALLPQALKHGNPLQLRRLLDG 521
           VG +AI RF+RPVCYQD+PDALLP AL+ GNPL L RL+DG
Sbjct: 480 VGASAIDRFVRPVCYQDLPDALLPAALQDGNPLGLTRLVDG 520


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: 813
Number of extensions: 28
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: 525
Length adjustment: 35
Effective length of query: 490
Effective length of database: 490
Effective search space:   240100
Effective search space used:   240100
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 2024 update 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