GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Burkholderia phytofirmans PsJN

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate BPHYT_RS22430 BPHYT_RS22430 succinate-semialdehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS22430 BPHYT_RS22430
           succinate-semialdehyde dehydrogenase
          Length = 486

 Score =  318 bits (816), Expect = 2e-91
 Identities = 170/461 (36%), Positives = 260/461 (56%), Gaps = 1/461 (0%)

Query: 10  YIDGQFVTWRGDAWIDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERA 69
           YI G++         +V NPAT   I+ +P     + R+AID A  A P W A  A +RA
Sbjct: 17  YIAGEWQGADDGTTFEVKNPATGETIATVPRMGTAETRRAIDTANAAWPAWRATTAKQRA 76

Query: 70  SWLRKISAGIRERASEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQS 129
             LRK    + E A +++ ++  E GK    A+ E+ + A ++++ AE  +R  G+ I +
Sbjct: 77  VILRKWHDLMMENADDLAKILTTEQGKPLAEAKGEIQYAASFLEWFAEEGKRVNGDTIPT 136

Query: 130 DRPGENILLFKRALGVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFA 189
               + I++ K  +GV   I PWNFP  +I RK+ PAL  G  I++KP+E TP +A+A A
Sbjct: 137 PASDKRIVVTKEPIGVCAAITPWNFPAAMITRKVGPALAAGCPIIVKPAEATPLSALALA 196

Query: 190 KIVDEIGLPRGVFNLVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVC 249
            + +  G+PRGVFN+V G  + +G E+ GNP V  +S TGS   G  +MA  A  + KV 
Sbjct: 197 VLAERAGVPRGVFNVVTGEPKAIGAEMTGNPIVRKLSFTGSTPVGRLLMAQCAPTVKKVS 256

Query: 250 LELGGKAPAIVMDDADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAM 309
           LELGG AP IV DDADL+ AV   + S+  NSGQ C C  R YV   +YD F  +L  A+
Sbjct: 257 LELGGNAPFIVFDDADLDAAVAGAIASKYRNSGQTCVCTNRFYVHDKVYDAFAEKLRVAV 316

Query: 310 QAVQFGNPAERNDIAMGPLINAAALERVEQKVARAVEEGARVAFGGKAVEGKGYYYPPTL 369
           + ++ G   E + +  GPLIN AA+ +VE  +  A+ +GAR+  GGK       ++ PT+
Sbjct: 317 EQLKVGRGTE-DGVTQGPLINDAAVLKVESHIEDALAKGARIVTGGKRHALGHGFFEPTV 375

Query: 370 LLDVRQEMSIMHEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKG 429
           L DV   M +  +ETFGP+ P+  F + E+ I +AND+++GL S  Y++++    +  + 
Sbjct: 376 LADVTPAMKVARDETFGPLAPLFRFSSDEEVIRLANDTEFGLASYFYSRDIGRVWRVAEA 435

Query: 430 LKFGETYINRENFEAMQGFHAGWRKSGIGGADGKHGLHEYL 470
           L++G   IN            G ++SG+G     +G+ +Y+
Sbjct: 436 LEYGMVGINTGLISNEVAPFGGVKQSGLGREGSHYGIDDYV 476


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: 542
Number of extensions: 21
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: 486
Length adjustment: 34
Effective length of query: 445
Effective length of database: 452
Effective search space:   201140
Effective search space used:   201140
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