GapMind for catabolism of small carbon sources

 

Alignments for a candidate for etoh-dh-nad in Gracilibacillus halophilus YIM-C55.5

Align alcohol dehydrogenase (EC 1.1.1.1) (characterized)
to candidate WP_003463377.1 J416_RS01495 glutathione-dependent formaldehyde dehydrogenase

Query= BRENDA::B2ZRE3
         (347 letters)



>NCBI__GCF_000359605.1:WP_003463377.1
          Length = 377

 Score =  215 bits (547), Expect = 2e-60
 Identities = 126/375 (33%), Positives = 196/375 (52%), Gaps = 32/375 (8%)

Query: 1   MRAVVFENKERVAVKEVNAPRLQHPLDALVRVHLAGICGSDLHLYHGKIPVLPGSVLGHE 60
           M++V ++ K  VAV +V  P ++   D +V++    ICGSDLHLY G  P+  G  +GHE
Sbjct: 1   MKSVTYQGKYEVAVTQVPFPTIEDDEDVIVKITSTAICGSDLHLYQGNFPLPIGYQIGHE 60

Query: 61  FVGQVEAVGEGIQDLQPGDWVVGPFHIACGTCPYCRRHQYNLCER-------GGVYGYGP 113
            +G VE VG  +  ++ GD VV PF IACG CPYC+ H  + C++       GG  GY  
Sbjct: 61  PMGIVEEVGPKVTKVKKGDRVVIPFTIACGQCPYCKTHHESQCDQANPHYDSGGYLGYSE 120

Query: 114 MFGNLQGAQAEILRVPFSNVNLRKLPPN--LSPERAIFAGDILSTAYGGLIQGQLRPGDS 171
            FGN  G QAE LRVPF N     +P +  L     +F  D+L TA   +    ++ GD+
Sbjct: 121 KFGNYPGGQAEYLRVPFGNYTPFLIPEDCELDDASLLFLSDVLPTALWSVEHAGVKAGDT 180

Query: 172 VAVIGAGPVGLMAIEVAQVLGASKILAIDRIPERLERAASLGAIPI-NAEQENPVRRVRS 230
           V V+G GP+GLM  + A    A++++A+D IP RLE A     + + N  Q + +     
Sbjct: 181 VIVLGCGPIGLMVQKFAWQKRANRVIAVDYIPYRLEHARKENRVEVFNFTQYDDMGETLK 240

Query: 231 ETNDEGPDLVLEAV--------------------GGAATLSLALEMVRPGGRVSAVGVDN 270
           E  + G D+V++ V                    G    + +A + V+  G V   GV  
Sbjct: 241 EITNGGADVVIDCVGMDGKKSPLEFVEQKTKLQGGTIGPIQIATKAVKKCGVVQMTGVYG 300

Query: 271 APSFPFPLASGLVKDLTFRIGLANVHLYIDAVLALLASGRLQPERIVSHYLPLEEAPRGY 330
                FPL +   +++  ++G A+   Y+ ++   + +G + P  I++H LPLE+A  GY
Sbjct: 301 GNYNLFPLGAFFSRNVQLKMGQAHARSYMASIYRQIVNGDIDPTTIITHQLPLEDASHGY 360

Query: 331 ELFDRKE--ALKVLL 343
           ++F+ K+   +KV+L
Sbjct: 361 DIFNGKKENCMKVVL 375


Lambda     K      H
   0.321    0.141    0.420 

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: 350
Number of extensions: 9
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: 347
Length of database: 377
Length adjustment: 29
Effective length of query: 318
Effective length of database: 348
Effective search space:   110664
Effective search space used:   110664
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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