GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Moritella dasanensis ArB 0140

Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate WP_017219751.1 A923_RS0100900 iron-containing alcohol dehydrogenase

Query= metacyc::STM4044-MONOMER
         (382 letters)



>NCBI__GCF_000276805.1:WP_017219751.1
          Length = 389

 Score =  219 bits (557), Expect = 1e-61
 Identities = 133/374 (35%), Positives = 204/374 (54%), Gaps = 12/374 (3%)

Query: 14  GAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEVFPNPTE 73
           G G I D+            L++TD  L  L ++ +      +  +   +F ++  NPT 
Sbjct: 19  GIGRIEDLPAACQELGMTSPLLITDPGLADLPMVQTALINCQKAGLKCGIFSQIKGNPTG 78

Query: 74  ELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVG----KVKNAG 129
           + +  G  A++  E D +IAFGGGS +D  KAV ++     P   +  VG    KV  AG
Sbjct: 79  DNISDGVRAFKGGEHDGVIAFGGGSALDAGKAVALMVGQDRPIWDFDDVGDNWLKVNAAG 138

Query: 130 -VPLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTA 188
            VP+VA+ TT+GT +E+   +VI DS   +K +I  PN++P I + D  + + +PA +TA
Sbjct: 139 MVPVVAVPTTSGTGSEVGRASVITDSNNHIKRIIFHPNMLPAIVILDPQLSVGLPAKLTA 198

Query: 189 ATGMDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYL 248
           ATG+DAL+HA+EAY + G HP+ +  ALE IRLI  +LP+AV+DG +LEAR QM     +
Sbjct: 199 ATGLDALSHALEAYCANGYHPMAEGIALEGIRLIKEYLPRAVEDGCDLEARAQMMTASTM 258

Query: 249 AGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFARIAQAMGV 308
              AF   GLG +HALAH  GA ++  HG+ NAIL+P V   NR    A+  R+++ + +
Sbjct: 259 GSTAF-QRGLGGMHALAHPIGALYDSHHGLLNAILMPYVLKANRSAIEAKLTRLSRYLAL 317

Query: 309 ETRGMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADPCAPCNPRT 368
           E      +A     +  I TL K++ IP    ++G+  + +      A  DP A  NP  
Sbjct: 318 E------DADFDGFLEWILTLRKQLDIPHSLGEIGIDADRVVEIGAMAEQDPSAGGNPIM 371

Query: 369 ASRDEVRGLYLEAL 382
            +  +   ++L A+
Sbjct: 372 LNAQQYADIFLSAV 385


Lambda     K      H
   0.317    0.133    0.384 

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: 412
Number of extensions: 25
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: 382
Length of database: 389
Length adjustment: 30
Effective length of query: 352
Effective length of database: 359
Effective search space:   126368
Effective search space used:   126368
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 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