Alignments for a candidate for xacF in Stenotrophomonas chelatiphaga DSM 21508

GapMind for catabolism of small carbon sources

Alignments for a candidate for xacF in Stenotrophomonas chelatiphaga DSM 21508

Align Alpha-ketoglutaric semialdehyde dehydrogenase; alphaKGSA dehydrogenase; 2,5-dioxovalerate dehydrogenase; EC 1.2.1.26 (characterized)
to candidate WP_057687530.1 ABB28_RS16890 betaine-aldehyde dehydrogenase

Query= SwissProt::P42236
         (488 letters)



>NCBI__GCF_001431535.1:WP_057687530.1
          Length = 490

 Score =  318 bits (815), Expect = 3e-91
 Identities = 185/489 (37%), Positives = 270/489 (55%), Gaps = 9/489 (1%)

Query: 1   MSVITEQNTYLNFINGEWVKSQSGDMVKVENPADVNDIVGYVQNSTAEDVERAVTAANEA 60
           MS +  Q  Y   I+G+ V + SG   +  NPA    ++  VQ +   DVERAV +A E 
Sbjct: 1   MSTLPLQQLY---IHGKLVDATSGKTFQSINPA-TGKVIAEVQIANQADVERAVASAAEG 56

Query: 61  KTAWRKLTGAERGQYLYKTADIMEQRLEEIAACATREMGKTLPEAKG-ETARGIAILRYY 119
           +  W  +T  ER + L +  D++ +R + +A   T + GK L E    +   G  +L YY
Sbjct: 57  QKVWAAMTAMERSRILRRAVDLLRERNDALAQLETLDTGKALSETTTVDIVTGADVLEYY 116

Query: 120 AGEGMRKTGDVIPSTDKDALMFTTRVPLGVVGVISPWNFPVAIPIWKMAPALVYGNTVVI 179
           AG      G+ +P  +  +  +T R PLGVV  I  WN+PV I +WK APAL  GN +V 
Sbjct: 117 AGLATAIEGNQVPLRES-SFFYTRREPLGVVAGIGAWNYPVQIALWKSAPALAAGNAMVF 175

Query: 180 KPATETAVTCAKIIACFEEAGLPAGVINLVTGPGSVVGQGLAEHDGVNAVTFTGSNQVGK 239
           KP+  T +T  ++   + EAG+P GV N+V GPG  VGQ L EH  +  ++FTG  + GK
Sbjct: 176 KPSEVTPLTVIELAKIYTEAGVPDGVFNVVQGPGREVGQWLTEHPVIEKISFTGGVETGK 235

Query: 240 -IIGQAALARGAKYQLEMGGKNPVIVADDADLEAAAEAVITGAFRSTGQKCTATSRVIVQ 298
            ++  AA +   +  +E+GGK+P+++ DDA LE AA+  +   F S+GQ CT  +RV V 
Sbjct: 236 KVMASAASSSLKEVTMELGGKSPLVICDDAQLERAADIAVMANFFSSGQVCTNGTRVFVP 295

Query: 299 SGIYERFKEKLLQRTKDITIGDSLKEDVWMGPIASKNQLDNCLSYIEKGKQEGASLLIGG 358
             +   F+  +++R K I IGD        GP+ S   +DN L  IE GK+EGA LL GG
Sbjct: 296 RPMLAAFEAAVVERVKRIRIGDPQDAQTNFGPMTSFAHMDNVLRLIETGKREGARLLTGG 355

Query: 359 EKLENGKYQNGYYVQPAIFDNVTSEMTIAQEEIFGPVIALIKVDSIEEALNIANDVKFGL 418
            +  +G    G YV P +F +   +MTI +EEIFGPV++++  D  EE +  AND  FGL
Sbjct: 356 GRATDGALAKGAYVLPTVFSDCRDDMTIVREEIFGPVMSILAYDDEEEVIARANDTHFGL 415

Query: 419 SASIFTENIGRMLSFIDEIDAGLVRINAESAGVELQAPFGGMKQSSSHSREQGEAAKDFF 478
           +A + + +I R    I  ++AG+  IN        + P GG KQS    RE G +    +
Sbjct: 416 AAGVVSNDIARAHRIIHRLEAGICWINTWGES-PAEMPVGGYKQSGV-GRENGISTLAHY 473

Query: 479 TAIKTVFVK 487
           T IK+V V+
Sbjct: 474 TRIKSVQVE 482


Lambda     K      H
   0.315    0.132    0.374 

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: 540
Number of extensions: 23
Number of successful extensions: 3
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: 488
Length of database: 490
Length adjustment: 34
Effective length of query: 454
Effective length of database: 456
Effective search space:   207024
Effective search space used:   207024
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 (21.5 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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Protein sequences (fasta format)
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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