GapMind for catabolism of small carbon sources

 

Alignments for a candidate for amaB in Acidovorax sp. GW101-3H11

Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate Ac3H11_1605 Aldehyde dehydrogenase B (EC 1.2.1.22)

Query= uniprot:Q92L07
         (510 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1605
          Length = 511

 Score =  726 bits (1873), Expect = 0.0
 Identities = 365/502 (72%), Positives = 421/502 (83%), Gaps = 2/502 (0%)

Query: 10  VASEAAALLDKMGVAKDLYTGGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAFRAW 69
           + SE   LL ++GV +  YTGG + + SP+TGE +A +   SAA+A   I +A  AF AW
Sbjct: 10  LVSEVDQLLQRLGVPRAAYTGGTLAARSPITGEVLAQVPQQSAADATAAIGRAHAAFLAW 69

Query: 70  RLVPAPKRGELVRLLGEELRAFKADLGRLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSR 129
           R VPAP+RGELVRLLGEELRA K DLG LV+IEAGKIPSEGLGEVQEMIDICDFAVGLSR
Sbjct: 70  RNVPAPRRGELVRLLGEELRAAKGDLGLLVTIEAGKIPSEGLGEVQEMIDICDFAVGLSR 129

Query: 130 QLYGLTIATERPGHRMMETWHPLGVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEK 189
           QLYGLTIATERPGHRMMETWHPLGV G+ISAFNFPVAVWSWNAALALVCGD+VVWKPSEK
Sbjct: 130 QLYGLTIATERPGHRMMETWHPLGVCGVISAFNFPVAVWSWNAALALVCGDSVVWKPSEK 189

Query: 190 TPLTALACQAILERAIARFG-DAPEGLSQVLIGDRAIGEVLVDHPKVPLVSATGSTRMGR 248
           TPLTALA  AI +RAIARFG DAPEGL ++++G R IGEVLVD  +VP++SATGST MGR
Sbjct: 190 TPLTALATHAIAQRAIARFGTDAPEGLLELIVGQRDIGEVLVDDARVPVLSATGSTAMGR 249

Query: 249 EVGPRLAKRFARAILELGGNNAGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHE 308
            VGPRLA RFAR ILELGGNNA IV P+ADL++ALR IAF AMGTAGQRCTTLRRLFVH 
Sbjct: 250 AVGPRLAARFARGILELGGNNAAIVAPTADLNLALRGIAFAAMGTAGQRCTTLRRLFVHA 309

Query: 309 SVYDQLVPRLKKAYQSVSVGNPLESAALVGPLVDKAAFDGMQKAIAEAKNHGGAVTGGER 368
           S+YDQLVP+L K Y +V VG+P     LVGPL+D+ AFDGMQKA+ +++  G  V GG R
Sbjct: 310 SIYDQLVPQLAKVYANVQVGDPRTPGTLVGPLIDRMAFDGMQKALEQSRALGATVHGGGR 369

Query: 369 VE-LGHENGYYVKPALVEMPKQEGPVLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSS 427
           VE +G  + YYV+PALVE+ K EGP L ETFAPILYV++YS  D  +A +NAV AGLSSS
Sbjct: 370 VEGVGGADAYYVRPALVELQKHEGPALHETFAPILYVVRYSAIDEAIAMNNAVGAGLSSS 429

Query: 428 IFTRDMQESERFLAADGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKAYMR 487
           IFT +++E+E+F++A GSDCGIANVNIG SGAEIGGAFGGEKETGGGRE+GSD+WKAYMR
Sbjct: 430 IFTLNVREAEQFMSAAGSDCGIANVNIGPSGAEIGGAFGGEKETGGGREAGSDSWKAYMR 489

Query: 488 RATNTVNYSKALPLAQGVSFDI 509
           RATNT+NYS ALPLAQGV+FD+
Sbjct: 490 RATNTINYSTALPLAQGVTFDV 511


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: 811
Number of extensions: 31
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: 510
Length of database: 511
Length adjustment: 35
Effective length of query: 475
Effective length of database: 476
Effective search space:   226100
Effective search space used:   226100
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 17 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