GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Rhizobium etli CFN 42

Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate WP_011427241.1 RHE_RS20725 aldehyde dehydrogenase family protein

Query= uniprot:Q92L07
         (510 letters)



>NCBI__GCF_000092045.1:WP_011427241.1
          Length = 512

 Score =  750 bits (1936), Expect = 0.0
 Identities = 376/507 (74%), Positives = 425/507 (83%), Gaps = 4/507 (0%)

Query: 8   IDVASEAAALLDKMGVAKDLYTGGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAFR 67
           +D+A+E A LL ++GV    Y GG +   SPVTG++I  L+  + +E    IE+A +AF 
Sbjct: 6   LDLATETAKLLAELGVDAGRYHGGTLSVTSPVTGKEIGKLREHTVSETKAAIEEAHKAFL 65

Query: 68  AWRLVPAPKRGELVRLLGEELRAFKADLGRLVSIEAGKIPSEGLGEVQEMIDICDFAVGL 127
            WR VPAPKRGELVRLLGEELRA K  LGRLVSIE GKI SEGLGEVQEMIDICDFAVGL
Sbjct: 66  EWRDVPAPKRGELVRLLGEELRAAKTALGRLVSIEVGKITSEGLGEVQEMIDICDFAVGL 125

Query: 128 SRQLYGLTIATERPGHRMMETWHPLGVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPS 187
           SRQLYGLTIATER  HRMME+WHPLG +GIISAFNFPVAVWSWNAALA+VCG++ VWKPS
Sbjct: 126 SRQLYGLTIATERSEHRMMESWHPLGAIGIISAFNFPVAVWSWNAALAMVCGNSTVWKPS 185

Query: 188 EKTPLTALACQAILERAIARF----GDAPEGLSQVLIGDRAIGEVLVDHPKVPLVSATGS 243
           EKTPLTALA QA+ E+A+ RF    G AP  LS ++IG R +GEVLVDHPK+PLVSATGS
Sbjct: 186 EKTPLTALAVQALFEKALKRFVAEGGKAPANLSTLIIGGREVGEVLVDHPKIPLVSATGS 245

Query: 244 TRMGREVGPRLAKRFARAILELGGNNAGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRR 303
           T MGR VGPRL++RFARAILELGGNNA IVCPSADLD+ LR +AF AMGTAGQRCTTLRR
Sbjct: 246 TAMGRAVGPRLSQRFARAILELGGNNAAIVCPSADLDLTLRGVAFSAMGTAGQRCTTLRR 305

Query: 304 LFVHESVYDQLVPRLKKAYQSVSVGNPLESAALVGPLVDKAAFDGMQKAIAEAKNHGGAV 363
           LFVH+SVYDQLVPRL+KAY SV++GNPLE+  LVGPL+D  AF+ MQ A+ EAK+ GG V
Sbjct: 306 LFVHDSVYDQLVPRLQKAYGSVTIGNPLEAGTLVGPLIDGQAFEKMQAALGEAKSAGGKV 365

Query: 364 TGGERVELGHENGYYVKPALVEMPKQEGPVLEETFAPILYVMKYSDFDAVLAEHNAVAAG 423
           TGGERV+ G  + +YV+PALVEMP Q GPV  ETFAPILYVMKYSDFDAVLA HNAV  G
Sbjct: 366 TGGERVDNGSADAFYVRPALVEMPAQTGPVEHETFAPILYVMKYSDFDAVLALHNAVPQG 425

Query: 424 LSSSIFTRDMQESERFLAADGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWK 483
           LSSSIFT DM+E+E F++A GSDCGIANVN+G SGAEIGGAFGGEKETGGGRESGSDAWK
Sbjct: 426 LSSSIFTNDMREAETFVSARGSDCGIANVNLGPSGAEIGGAFGGEKETGGGRESGSDAWK 485

Query: 484 AYMRRATNTVNYSKALPLAQGVSFDIE 510
           AYMRRATNT+NY   LPLAQGV FD+E
Sbjct: 486 AYMRRATNTINYGSTLPLAQGVKFDVE 512


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: 856
Number of extensions: 41
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: 510
Length of database: 512
Length adjustment: 35
Effective length of query: 475
Effective length of database: 477
Effective search space:   226575
Effective search space used:   226575
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 Apr 09 2024. 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