GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Pseudomonas fluorescens GW456-L13

Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate PfGW456L13_3209 Butyryl-CoA dehydrogenase (EC 1.3.99.2)

Query= reanno::acidovorax_3H11:Ac3H11_2996
         (376 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3209
          Length = 386

 Score =  264 bits (675), Expect = 3e-75
 Identities = 156/381 (40%), Positives = 226/381 (59%), Gaps = 13/381 (3%)

Query: 3   LTQDQEMIRDAVRDFAQTELWPHAARWDKEHHF-PKDAHQ--GLAAL-GAYGICVPEEFG 58
           LTQ+QEM+ D+VR F + EL P+  + D+     P+ A Q  G A + G Y   +PEE G
Sbjct: 5   LTQEQEMLVDSVRSFVEKELLPYEEQVDRADEVSPELAAQIRGKAIVAGFYAFNMPEEVG 64

Query: 59  GANLDYLTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGNAQQKRDWLTPLARGEML 118
           G  LDYL+ AL+  E++      S A+ V     + ILM     +Q  D+L P  +GE +
Sbjct: 65  GGGLDYLSQALIERELSK----VSWALHVFVARPSKILMAC-KGEQINDYLLPCIQGEKI 119

Query: 119 GAFCLTEPHVGSDASALRTTAVKQGDEYVINGVKQFITSGKNGQVAIVIAVTD----KGA 174
             F LTEP  GSDA+A++T AV++GD++++NG K FI+   +   AIV AVTD     G 
Sbjct: 120 DCFALTEPGAGSDANAIKTRAVREGDDFILNGSKHFISHAGHADFAIVFAVTDTYEHNGK 179

Query: 175 GKKGMSAFLVPTNNPGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIGAEGEGYKIAL 234
            +  +++FLV  N PG  + R    +      T ++ FD+CR+PA  ++G  G+G+ +A 
Sbjct: 180 KRNAVTSFLVDRNTPGMTIRRGPKCVSNRGYHTFEMFFDDCRVPASKVLGEVGKGWDVAN 239

Query: 235 GALEGGRIGIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADCATQIEAAR 294
             L  GR+ +AA  VG A+ A D +L ++ +R+ FG  I  +Q V F+LAD ATQI AA 
Sbjct: 240 AWLTAGRVMVAANCVGQAQRALDVSLQWAADRKQFGQPIGTYQGVSFKLADMATQIRAAE 299

Query: 295 QLIWHAAALRDAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFPVERIYRDV 354
            L  H A   D G     EA MAKLFASE+  R    A+Q  GG G++++ PVERI+R+ 
Sbjct: 300 LLTLHTAWKMDQGTMTDGEAGMAKLFASEVLGRTADEAVQIFGGMGLMDEGPVERIWRNA 359

Query: 355 RVCQIYEGTSDVQKIIIQRAL 375
           R+ +I+EGTS++Q+ II R L
Sbjct: 360 RIERIWEGTSEIQRHIISREL 380


Lambda     K      H
   0.319    0.134    0.396 

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: 334
Number of extensions: 15
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: 376
Length of database: 386
Length adjustment: 30
Effective length of query: 346
Effective length of database: 356
Effective search space:   123176
Effective search space used:   123176
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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