GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Paucidesulfovibrio gracilis DSM 16080

Align Lactaldehyde reductase (characterized, see rationale)
to candidate WP_078716111.1 B5D49_RS02645 iron-containing alcohol dehydrogenase

Query= uniprot:Q8A199
         (384 letters)



>NCBI__GCF_900167125.1:WP_078716111.1
          Length = 382

 Score =  245 bits (626), Expect = 1e-69
 Identities = 147/371 (39%), Positives = 215/371 (57%), Gaps = 8/371 (2%)

Query: 12  FGAGCRSVIAVEAARRGFKKAFFVTDKDL-IKFGVAAEIIKVFDDNHIPYELYSDVKANP 70
           FG G  + +  E AR G  +A  VT K    + G    +    ++  +   L+++V+++P
Sbjct: 14  FGNGAVAQVGRETARLG-SRALIVTGKSSSTRTGSLEAVTASLNEAGVHPVLFAEVESDP 72

Query: 71  TIANVQNGVAAYKASGADFIVALGGGSSIDTAKGIGIVVNNP-DFADVKSLEGVADTKHK 129
           +I  V+ G A  + +  D IV LGGGS +D AKGI +++ +P D  D  S          
Sbjct: 73  SIQTVEAGAALARENQCDVIVGLGGGSPLDAAKGIVLLLTHPGDIRDYTS----QPADGP 128

Query: 130 AVPTFALPTTAGTAAEVTINYVIIDEDARKKMVCVDPNDIPAVAIVDPELMYSMPKGLTA 189
            +P  ++PTTAGTA+E+T   VI D + + KM       IP+VA++DP+L  +MP+ +TA
Sbjct: 129 GMPLISIPTTAGTASEITRFTVITDTEQKIKMSLQGTALIPSVALLDPQLTVTMPQHVTA 188

Query: 190 ATGMDALTHAIESYITPGAWAMSDMFELKAIEMIAQNLKAAVDNGKDTVAREAMSQAQYI 249
           ATGMDALTHAIE+YI+  A  MSD+  L+AI +I  NL  AVD+  +  AREAM + Q  
Sbjct: 189 ATGMDALTHAIEAYISKLATPMSDLHALEAIRLIGANLIKAVDSPDNMAAREAMLRGQMH 248

Query: 250 AGMGFSNVGLGIVHSMAHPLGAFYDTPHGVANALLLPYVMEYNAESPAAPKYIHIAKAMG 309
           AG+ FSN  + +VHSM+ PLGA +   HG ANA+LLP VM++N  S AA +Y HIA+A+G
Sbjct: 249 AGLAFSNASVALVHSMSRPLGALFGIAHGQANAMLLPVVMDFN-RSAAADRYRHIAEALG 307

Query: 310 VNTDGMTETEGVKAAIEAVKALSLSIGIPQKLHEINVKEEDIPALAVAAFNDVCTGGNPR 369
            N   ++  +  K  + +V+ L    G+ Q L    V+E+DI  LA  A     T  NPR
Sbjct: 308 ENVQELSARDAAKTTVLSVEELFEETGLEQHLSAYGVQEKDIARLAKDAMESASTAFNPR 367

Query: 370 PTSVAEIEVLY 380
              +  +  +Y
Sbjct: 368 KADLESVAAIY 378


Lambda     K      H
   0.317    0.133    0.379 

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: 326
Number of extensions: 15
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: 384
Length of database: 382
Length adjustment: 30
Effective length of query: 354
Effective length of database: 352
Effective search space:   124608
Effective search space used:   124608
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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