GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Phaeobacter inhibens BS107

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate GFF2918 PGA1_c29650 succinate-semialdehyde dehdyrogenase GabD

Query= BRENDA::P25553
         (479 letters)



>lcl|FitnessBrowser__Phaeo:GFF2918 PGA1_c29650
           succinate-semialdehyde dehdyrogenase GabD
          Length = 491

 Score =  303 bits (775), Expect = 1e-86
 Identities = 171/467 (36%), Positives = 249/467 (53%), Gaps = 3/467 (0%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           YI G FV    D    V NPA   VI+ + D        AI  AE AQ +W      ERA
Sbjct: 23  YIGGAFVDG-ADGTFAVKNPARGDVIANVADVSRSQVAGAIAQAEVAQKDWAKWTGKERA 81

Query: 70  SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129
           + LRK    + E   +++ ++  E GK    +  E+ + A +I++ AE A+R  GE I  
Sbjct: 82  NVLRKWFDLMMENQEDLAVILTAEMGKPLAESRGEIGYGASFIEFFAEEAKRIYGETIPG 141

Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189
            +  + I + K+ +GV   I PWNFP  +I RK  PAL  G   V +P+E TP +A A A
Sbjct: 142 HQRDKRITVLKQPIGVAASITPWNFPNAMITRKAGPALAAGCAFVARPAELTPLSATALA 201

Query: 190 KIVDEIGLPRGVFNLVL-GRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKV 248
            + D  G+P GVFN+V        G+E   N  V  ++ TGS   G  +M  AA  + K 
Sbjct: 202 VLADRAGIPAGVFNVVTSSNASETGKEFCENNAVRKLTFTGSTEVGRILMRQAADTVMKC 261

Query: 249 CLELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEA 308
            +ELGG AP IV DDADL+ AV+  +  +  N+GQ C CA R+YVQ G+YD F  +L EA
Sbjct: 262 SMELGGNAPFIVFDDADLDAAVEGAIMCKFRNNGQTCVCANRIYVQAGVYDAFAAKLKEA 321

Query: 309 MQAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPT 368
           +  +  G+         GPLIN  A+E+V+  +A A E+GA V  GG   E  G ++ PT
Sbjct: 322 VAKMTVGDGLAEG-TQFGPLINEKAVEKVQAHIADAKEKGAEVILGGNPSELGGTFFEPT 380

Query: 369 LLLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIK 428
           ++    Q+M    +ETFGP+ P+  F+T +D I MAND+ +GL S  Y ++L+   K  +
Sbjct: 381 IITGATQDMVFSQDETFGPMAPLFKFETEDDVIEMANDTIFGLASYFYAKDLSRVYKVAE 440

Query: 429 GLKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVV 475
            L++G   +N            G ++SG+G     HG+ +YL+ + +
Sbjct: 441 ALEYGIVGVNTGIISTELAPFGGVKQSGLGREGSHHGIEDYLEMKYI 487


Lambda     K      H
   0.318    0.135    0.392 

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: 537
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: 479
Length of database: 491
Length adjustment: 34
Effective length of query: 445
Effective length of database: 457
Effective search space:   203365
Effective search space used:   203365
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