GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aldA in Paraburkholderia bryophila 376MFSha3.1

Align lactaldehyde dehydrogenase (EC 1.2.1.22); D-glyceraldehyde dehydrogenase (NADP+) (EC 1.2.1.89) (characterized)
to candidate H281DRAFT_00972 H281DRAFT_00972 lactaldehyde dehydrogenase / glycolaldehyde dehydrogenase

Query= BRENDA::P25553
         (479 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_00972 H281DRAFT_00972
           lactaldehyde dehydrogenase / glycolaldehyde
           dehydrogenase
          Length = 481

 Score =  411 bits (1057), Expect = e-119
 Identities = 205/458 (44%), Positives = 296/458 (64%), Gaps = 5/458 (1%)

Query: 24  IDVVNPATEAVISRIPDGQAEDARKAIDAAERAQPEWEALPAIERASWLRKISAGIRERA 83
           I V NPATEA+I+ +      D   A+DAA  AQ  W  LP+ ER ++L K++  + E A
Sbjct: 25  IAVYNPATEALIAHVTAASHADVIAAVDAAAVAQKAWRKLPSAERGAYLHKLADTLTECA 84

Query: 84  SEISALIVEEGGKIQQLAEVEVAFTADYIDYMAEWARRYEGEIIQSDRPGENILLFKRAL 143
            +I A +  E GK    A  E  +      Y AEWARR EGE+I SD P EN++L +  +
Sbjct: 85  PDIGAALALESGKSVADATSEAVYAGQITRYHAEWARRIEGEVIPSDSPDENLVLHREPI 144

Query: 144 GVTTGILPWNFPFFLIARKMAPALLTGNTIVIKPSEFTPNNAIAFAKIVDEIGLPRGVFN 203
           GV   ++P+N+P +   RK+APAL+ GNT+V++PS  TP +A   A+ V++ GLP GV N
Sbjct: 145 GVVACLIPFNYPVYTFMRKVAPALIAGNTVVVRPSNNTPTSAFEIARAVEKAGLPAGVVN 204

Query: 204 LVLGRGETVGQELAGNPKVAMVSMTGSVSAGEKIMATAAKNITKVCLELGGKAPAIVMDD 263
            +L       + L  +P++ M+++TGSV AG K++    +NI K  LELGGK PAI+  D
Sbjct: 205 -ILAMNHATAEALCTHPRIGMITLTGSVGAGRKVLEYCKENIAKPSLELGGKTPAIIEAD 263

Query: 264 ADLELAVKAIVDSRVINSGQVCNCAERVYVQKGIYDQFVNRLGEAMQAVQFGNPAERNDI 323
           ADLE A + +V S+  + GQ+C   ERVYV + ++D+FV  L   M AV+FG+ +E+  +
Sbjct: 264 ADLERAARELVASKTTHCGQLCTAIERVYVHESVHDRFVALLKRHMSAVEFGDRSEQPSL 323

Query: 324 AMGPLINAAALERVEQKVARAVEEGARVAFGGK---AVEGKGYYYPPTLLLDVRQEMSIM 380
            MGPL+N A+ + +   V RA+  GA +  GGK     EGKG++YP TLL + RQ+M I+
Sbjct: 324 -MGPLVNEASRQSIHAMVERAIAAGATLETGGKLPAPAEGKGFFYPATLLSNCRQDMEIV 382

Query: 381 HEETFGPVLPVVAFDTLEDAISMANDSDYGLTSSIYTQNLNVAMKAIKGLKFGETYINRE 440
            EETFGPV+PVV + TL++A+ MAND  +GL+S +YT+N   AMK   G++ GE Y+NR 
Sbjct: 383 QEETFGPVMPVVKYRTLDEALDMANDHQFGLSSVLYTENYRNAMKVANGIEAGELYVNRT 442

Query: 441 NFEAMQGFHAGWRKSGIGGADGKHGLHEYLQTQVVYLQ 478
             +  QGFHAGW++SG+GG DGKHG+ E+ QT++V ++
Sbjct: 443 PADPYQGFHAGWKRSGLGGDDGKHGMLEFTQTRLVVMK 480


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: 565
Number of extensions: 20
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: 479
Length of database: 481
Length adjustment: 34
Effective length of query: 445
Effective length of database: 447
Effective search space:   198915
Effective search space used:   198915
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: 51 (24.3 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