GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Streptacidiphilus oryzae TH49

Align 2-methyl-branched-chain-enoyl-CoA reductase (EC 1.3.8.5) (characterized)
to candidate WP_037571613.1 BS73_RS11870 acyl-CoA dehydrogenase

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



>NCBI__GCF_000744815.1:WP_037571613.1
          Length = 407

 Score =  253 bits (645), Expect = 9e-72
 Identities = 144/389 (37%), Positives = 230/389 (59%), Gaps = 17/389 (4%)

Query: 3   LTQDQEMIRDAVRDFAQTELWPHAARWDKEHHFPKDAHQGLAALGAYGICVPEEFGGANL 62
           LT+ Q  I   VRDF   E+ P A   +    +P    +G+  LG +G+ +PEEFGG   
Sbjct: 12  LTEVQRDILATVRDFVDKEIIPVATELEHRDEYPTKIVEGMKELGLFGLTIPEEFGGLGE 71

Query: 63  DYLTLALVLEEIAAGDGGTSTAISVTNCPVNAILMRYGNAQQKRDWLTPLARGEMLGAFC 122
             LT ALV+EEIA G    S  ++ T+  V  ++  +G  +QK  +L  +A GE+ GAF 
Sbjct: 72  SLLTYALVVEEIARGWMSVSGIVN-THFIVAHMINAHGTQEQKEYFLPRMAAGEVRGAFS 130

Query: 123 LTEPHVGSDASALRTTAVKQGD--EYVINGVKQFITSGKNGQVAIVIAVTDKG-----AG 175
           ++EP +GSD +A+RT AV+ G+  ++V+NG K ++T+G +  +  ++A TD+G     A 
Sbjct: 131 MSEPGLGSDVAAIRTKAVQDGEGGDWVVNGQKMWLTNGGSSTLVALLAHTDEGDPENTAA 190

Query: 176 KKGMSAFLVPTNN--------PGYVVARLEDKLGQHSSDTAQINFDNCRIPAENLIG-AE 226
            + M+ FL+            PG  V    +K+G    DT ++   + R+PA+ ++G A 
Sbjct: 191 HRNMTTFLIEKEPGFGENEKVPGLTVPGKIEKMGYKGVDTTELVLQDVRVPADRVLGGAS 250

Query: 227 GEGYKIALGALEGGRIGIAAQSVGMARSAFDAALAYSKERESFGTAIFNHQAVGFRLADC 286
           G G+   +  +E GR+ +AA+  G+AR AF+  +AY+++RE+FG  I  HQA+ F+LA+ 
Sbjct: 251 GRGFYQMMDGVEVGRVNVAARGCGVARRAFELGIAYAQQRETFGKKIAQHQAIQFKLAEM 310

Query: 287 ATQIEAARQLIWHAAALRDAGKPCLKEAAMAKLFASEMAERVCSAAIQTLGGYGVVNDFP 346
           AT++EAA Q++  AA  +D+G+    EA MAK  ASE  + V   A +  GGYG   ++ 
Sbjct: 311 ATKVEAAHQMMVMAARKKDSGERNDLEAGMAKYLASEYCKEVVEDAFRIHGGYGFSKEYE 370

Query: 347 VERIYRDVRVCQIYEGTSDVQKIIIQRAL 375
           +ER+YR+  +  I EGT+++QK+I+ R L
Sbjct: 371 IERLYREAPMLLIGEGTAEIQKMIVGRRL 399


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: 402
Number of extensions: 17
Number of successful extensions: 5
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: 407
Length adjustment: 31
Effective length of query: 345
Effective length of database: 376
Effective search space:   129720
Effective search space used:   129720
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 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