GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Rhodobacter viridis JA737

Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate WP_110806407.1 C8J30_RS13690 aldehyde dehydrogenase family protein

Query= uniprot:Q92L07
         (510 letters)



>NCBI__GCF_003217355.1:WP_110806407.1
          Length = 503

 Score =  746 bits (1927), Expect = 0.0
 Identities = 376/498 (75%), Positives = 420/498 (84%)

Query: 13  EAAALLDKMGVAKDLYTGGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLV 72
           E   LL ++GV    + GG M SFSP+TG +I +L   +    A  I +A  AFR WRLV
Sbjct: 6   ETRTLLCRLGVVPAAFEGGSMASFSPLTGAQIGALTPETPKSTAAAIARAAAAFRLWRLV 65

Query: 73  PAPKRGELVRLLGEELRAFKADLGRLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLY 132
           PAPKRGELVRL  EELRA KADLGRLVSIEAGK  SEGLGEVQEMIDICDFAVGLSRQLY
Sbjct: 66  PAPKRGELVRLWAEELRAAKADLGRLVSIEAGKSASEGLGEVQEMIDICDFAVGLSRQLY 125

Query: 133 GLTIATERPGHRMMETWHPLGVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPL 192
           GLTIATERPGHRMMETWHPLGVVG+ISAFNFPVAVW+WN ALALVCG+ V+WKPSEKTPL
Sbjct: 126 GLTIATERPGHRMMETWHPLGVVGVISAFNFPVAVWAWNTALALVCGNPVLWKPSEKTPL 185

Query: 193 TALACQAILERAIARFGDAPEGLSQVLIGDRAIGEVLVDHPKVPLVSATGSTRMGREVGP 252
           TALA QA+L RA+ARF  APEGL+Q+LIG   +G  LV+ PKV L+SATGSTRMGR VGP
Sbjct: 186 TALAAQAVLGRALARFDAAPEGLAQLLIGGPEVGAALVESPKVALISATGSTRMGRIVGP 245

Query: 253 RLAKRFARAILELGGNNAGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYD 312
           ++A RF R+ILELGGNNAGIVC SADLDM LRA+AFGAMGTAGQRCTTLRRLFVH+SVYD
Sbjct: 246 KVAARFGRSILELGGNNAGIVCASADLDMTLRAVAFGAMGTAGQRCTTLRRLFVHDSVYD 305

Query: 313 QLVPRLKKAYQSVSVGNPLESAALVGPLVDKAAFDGMQKAIAEAKNHGGAVTGGERVELG 372
            L+PRL +AY SVSVGNPLE+ ALVGPL+D+AAFD MQ A+  A   GG V GG RV  G
Sbjct: 306 TLMPRLIRAYASVSVGNPLETQALVGPLIDRAAFDAMQSALDAALAAGGIVHGGTRVACG 365

Query: 373 HENGYYVKPALVEMPKQEGPVLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRD 432
            ++ YYV+PALVEMP Q GPVLEETFAPILYVM++SD +AV+ EHNAVAAGLSS+IFT D
Sbjct: 366 PDSAYYVRPALVEMPAQIGPVLEETFAPILYVMRFSDLEAVIEEHNAVAAGLSSAIFTLD 425

Query: 433 MQESERFLAADGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKAYMRRATNT 492
           ++E E FL+A GSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWK YMRRATNT
Sbjct: 426 LREMETFLSAAGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYMRRATNT 485

Query: 493 VNYSKALPLAQGVSFDIE 510
           +N+S+ LPLAQGV FDIE
Sbjct: 486 INFSRDLPLAQGVVFDIE 503


Lambda     K      H
   0.317    0.134    0.390 

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: 870
Number of extensions: 34
Number of successful extensions: 1
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: 510
Length of database: 503
Length adjustment: 34
Effective length of query: 476
Effective length of database: 469
Effective search space:   223244
Effective search space used:   223244
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: 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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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:

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:

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:

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:

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