GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Burk376:H281DRAFT_00972
          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:

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