GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Pantoea rwandensis LMG 26275

Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate WP_084938278.1 HA51_RS25705 iron-containing alcohol dehydrogenase

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



>NCBI__GCF_002095475.1:WP_084938278.1
          Length = 382

 Score =  179 bits (455), Expect = 9e-50
 Identities = 115/369 (31%), Positives = 186/369 (50%), Gaps = 3/369 (0%)

Query: 12  LHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLFDEVFPNP 71
           + G  A+ D+  L+  K+  KAL+VTD  +  +  + SL + L +   S  + + V P P
Sbjct: 8   ISGFQALNDLSYLLQGKE--KALLVTDKNIEGIPAVQSLIAQLKQQISSLSIVNSVPPEP 65

Query: 72  TEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGKVKNAGVP 131
           ++  V    AA  S + D +I  GGGS +D AK + IL  +  P+      G+       
Sbjct: 66  SQHDVAAIVAALPSTDVDLVIGVGGGSVLDVAKLLSILCVDGAPTLDALLAGEKPQTRTT 125

Query: 132 LVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPASVTAATG 191
            + I TTAGT +E T NA++    ++ K  II P ++PD       +   +P  + ++TG
Sbjct: 126 SLLIPTTAGTGSEATPNAILAIPEKETKVGIITPVMLPDYVALVPELTTSMPPHIASSTG 185

Query: 192 MDALTHAVEAYVSVGAHPLTDANALEAIRLINLWLPKAVDDGHNLEAREQMAFGQYLAGM 251
           +DAL H +E + +  A+P++D  AL  ++ +   L   + +  NLEAR  M +  Y  G 
Sbjct: 186 IDALCHLIECFTATVANPVSDNYALIGMKKLFASLETTIAEPGNLEARLNMLWASYYGGA 245

Query: 252 AFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVENFNRPNAVARFARIAQAMGVETR 311
           +   AG  LVHA+++  G  ++LPHGV NAILL     F RP AV++FA+    +     
Sbjct: 246 SIAHAGTHLVHAMSYPLGGKYHLPHGVANAILLAPCMRFVRPAAVSKFAQAYDLLPDADA 305

Query: 312 GMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDIEGWLDKALADPCAPCN-PRTAS 370
            + +EA S   +     L KR+ +P    +LG+  + +   ++ AL       N P    
Sbjct: 306 TLDEEAKSHALVEYFAALVKRLKLPASLEELGIGPDHLPYLVEAALDVQRLMKNVPMKVG 365

Query: 371 RDEVRGLYL 379
            D+VR +YL
Sbjct: 366 ADDVRNVYL 374


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: 359
Number of extensions: 14
Number of successful extensions: 1
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: 382
Length adjustment: 30
Effective length of query: 352
Effective length of database: 352
Effective search space:   123904
Effective search space used:   123904
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