GapMind for catabolism of small carbon sources

 

Aligments for a candidate for amaB in Azospirillum brasilense Sp245

Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate AZOBR_RS09720 AZOBR_RS09720 succinate-semialdehyde dehdyrogenase

Query= uniprot:Q92L07
         (510 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS09720 AZOBR_RS09720
           succinate-semialdehyde dehdyrogenase
          Length = 497

 Score =  218 bits (555), Expect = 4e-61
 Identities = 149/464 (32%), Positives = 232/464 (50%), Gaps = 13/464 (2%)

Query: 26  DLYTGGDMPSFSPVTGEKIASLKTVSAAEAAGKIEKADEAFRAWRLVPAPKRGELVRLLG 85
           D  +G  +   +P  G  + S+  + A E    IE A+ A+ AWR + A +R + +R   
Sbjct: 32  DADSGKTVEVTNPADGSVLGSVPMMGADETRRAIEAAERAWPAWRALTAKERAKTLRTWF 91

Query: 86  EELRAFKADLGRLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHRM 145
           + + A + D+ R+++ E GK  +E  GEV       ++     +++YG TI    PG R+
Sbjct: 92  DLMMANQEDIARIMTAEQGKPLAEARGEVAYAASFIEWFAEEGKRVYGDTIPQHLPGRRI 151

Query: 146 METWHPLGVVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAI 205
           + T  P+GV   I+ +NFP A+ +  A  AL  G  +V KP+  TPLTALA   + ERA 
Sbjct: 152 VVTKEPIGVTAAITPWNFPAAMITRKAGPALAAGCPMVIKPATATPLTALAMAVLAERA- 210

Query: 206 ARFGDAPEGLSQVLIGD-RAIGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILE 264
                 P G+  V+ G  RAIG  +  +P V  ++ TGST +G+E+  + A    +  LE
Sbjct: 211 ----GIPAGILSVVTGSARAIGGEMTGNPTVRKLTFTGSTEIGKELMAQCAGTVKKVSLE 266

Query: 265 LGGNNAGIVCPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQS 324
           LGGN   +V   ADLD A++          GQ C    RL V   VYD    +L +A ++
Sbjct: 267 LGGNAPFLVFNDADLDEAVKGAIASKYRNTGQTCVCANRLLVQSGVYDAFAAKLAEAVKA 326

Query: 325 VSVGNPLES-AALVGPLVDKAAFDGMQKAIAEAKNHGG-AVTGGERVELGHENGYYVKPA 382
           + VG  L +  A  GPL+D AA + ++  I +A   G   V GG+R ELG    ++    
Sbjct: 327 LKVGPGLTTEGAQQGPLIDMAAVEKVEDHIRDATEKGARVVLGGKRHELG--GSFFEPTI 384

Query: 383 LVEMPKQEGPVLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAA 442
           L ++        EETF P+  + ++   +  +   NA   GL++  ++RD+    R   A
Sbjct: 385 LADVTPAMKVAREETFGPVAPLFRFETEEEAVRMANATEFGLAAYFYSRDIGRVWR--VA 442

Query: 443 DGSDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKAYM 486
           +  + GI  +N G    E+   FGG KE+G GRE      + Y+
Sbjct: 443 EALEYGIVGINEGIISTEV-APFGGMKESGIGREGSKYGIEDYL 485


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: 574
Number of extensions: 29
Number of successful extensions: 4
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: 497
Length adjustment: 34
Effective length of query: 476
Effective length of database: 463
Effective search space:   220388
Effective search space used:   220388
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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