GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fucO in Sinorhizobium meliloti 1021

Align L-lactaldehyde reductase (EC 1.1.1.77) (characterized)
to candidate SMa0263 SMa0263 alcohol dehydrogenase

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



>FitnessBrowser__Smeli:SMa0263
          Length = 399

 Score =  174 bits (442), Expect = 3e-48
 Identities = 133/394 (33%), Positives = 191/394 (48%), Gaps = 27/394 (6%)

Query: 5   LALPKISLHGAGAIADMVNLVANKQWGKALIVTDGQLVKLGLLDSLFSALDEHQMSYHLF 64
           L  P+  L GAG     +  +A K   +ALIVTD +L     L +L   L+E  +   + 
Sbjct: 7   LRAPRELLFGAGQ-RHALGGIAAKLGHRALIVTDTRLAVDADLLALVRRLEEAGLEVMVD 65

Query: 65  DEVFPNPTEELVQKGFAAYQSAECDYIIAFGGGSPIDTAKAVKILTANPGPSTAYSGVGK 124
               P+   E      AA      D +I  GGGS +D AK V +L  + G    Y G   
Sbjct: 66  SSTLPDVPVESAIVSAAAASGFAPDLVIGIGGGSCLDMAKCVTLLLTHGGRPQDYYGEYA 125

Query: 125 VKNAGVPLVAINTTAGTAAEMTSNAVIIDSARKVKEVIIDPNIIPDIAVDDASVMLEIPA 184
           V    +PL+AI TTAGT +E+T  AV+ D+ R +K  I  P++IP +++ D  + L  P 
Sbjct: 126 VPGPVMPLIAIPTTAGTGSEVTPVAVLSDAERSLKVGISSPHLIPAVSICDPELTLSCPP 185

Query: 185 SVTAATGMDALTHAVEAY---------------VSVGAHPLTDANALEAIRLINLWLPKA 229
            +TA  G DALTHA+EA+               V VG + L+D  AL AI L+   L +A
Sbjct: 186 GLTAIAGADALTHAIEAFTAIRREPVPGIAQQRVFVGKNELSDHFALSAITLLWQGLERA 245

Query: 230 VDDGHNLEAREQMAFGQYLAGMAFNSAGLGLVHALAHQPGATHNLPHGVCNAILLPIVEN 289
             DG +  ARE +  G  LAG+AF  AG    HA+ +  GA  +  HG+  A L+P V  
Sbjct: 246 CKDGADAGARETVMLGATLAGLAFGVAGTAAAHAIQYPVGALTHTAHGLGVACLMPYVMT 305

Query: 290 FNRPNAVARFARIAQAMGVETRGMSDEAASQEAINAIRTLSKRVGIPEGFSKLGVTKEDI 349
           +N P      A+IA A G+            E I A+ +L +R+GIP     LG+ ++ I
Sbjct: 306 WNAPLIRDELAQIAHAAGL--------GGPDEVIPALVSLFERIGIPATLRDLGLEEDRI 357

Query: 350 EGWLDKALAD--PCAPCNPRTASRDEVRGLYLEA 381
           + W+ +  +        NPR  +  E+R L   A
Sbjct: 358 D-WVAEQSSGIARLIQNNPRPLNPHEMRNLVAAA 390


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: 410
Number of extensions: 29
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: 382
Length of database: 399
Length adjustment: 31
Effective length of query: 351
Effective length of database: 368
Effective search space:   129168
Effective search space used:   129168
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 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