GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Phaeo:GFF2918
          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.

Links

Downloads

Related tools

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