GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuA in Methylibium petroleiphilum PM1

Align Isovaleryl-CoA dehydrogenase, mitochondrial; IVD; Isovaleryl-CoA dehydrogenase 2; St-IVD2; EC 1.3.8.4 (characterized)
to candidate WP_041929725.1 MPE_RS16000 acyl-CoA dehydrogenase

Query= SwissProt::Q9FS87
         (412 letters)



>NCBI__GCF_000015725.1:WP_041929725.1
          Length = 391

 Score =  208 bits (529), Expect = 3e-58
 Identities = 121/373 (32%), Positives = 193/373 (51%), Gaps = 7/373 (1%)

Query: 36  DTQKQFKESVAQFAQENIAPHAEKIDRTNYFPQDVNLWKLMGNFNLLGITVPEEYGGLGL 95
           + ++  +++   + ++ +AP    ++   +   D  +++ MG   LLG T+PE YGG GL
Sbjct: 19  EDERAVRDAAQAYCRDRLAPRV--LEAFRHEKTDPAIFREMGELGLLGATLPEAYGGAGL 76

Query: 96  GYLYHCIAMEEISRASGSVGLSYGAHTNLCINQLVRNGTHEQKQKYLPKLISGEHVGALA 155
            ++ + +   E+ R            ++L +  +   GT  QKQKYLPKL  GE +G   
Sbjct: 77  NHVCYGLVAREVERVDSGYRSMMSVQSSLVMVPIHAFGTEAQKQKYLPKLARGEWIGCFG 136

Query: 156 MSEPNAGSDVVSMKCKADRVEGGYVLNGNKMWCTNGPTAQTLVVYAKTDVTAGSKGITAF 215
           ++EPN GSD  S+  +A  V+GGYVL+G KMW TN P A   VV+AK D       I  F
Sbjct: 137 LTEPNHGSDPGSLATRARAVQGGYVLSGAKMWITNSPIADVFVVWAKDD----GGQIRGF 192

Query: 216 IIEKGMTGFSTAQKLDKLGMRGSDTCELVFENCFVPEENVLGQVGRGVYVLMSGLDLERL 275
           I++KGM G        K+G+R S T E+V +  F PEEN   +V RG+    + L+  R 
Sbjct: 193 ILDKGMKGLEAPAVHGKVGLRASLTGEIVMDEVFCPEENAFPEV-RGLKGPFTCLNSARY 251

Query: 276 VLASGPVGIMQACLDVVLPYVKQREQFGRPIGEFQFVQGKVADMYTSMQSSRSYLYSVAR 335
            +A G +G  + C      YV  R QFGRP+   Q +Q K+ADM T +         + R
Sbjct: 252 GIAWGALGAAEDCFHRARQYVLDRPQFGRPLAANQLIQKKLADMQTEITLGLQGCLRLGR 311

Query: 336 ECDSGTINTKDCAGVILSAAERATQVALQAIQCLGGNGYVNEYPTGRFLRDAKLYEIGAG 395
             D GT   +  + +  ++  ++ ++A  A   +GGNG  +E+   R L + ++     G
Sbjct: 312 MKDEGTAAVEITSIMKRNSCGKSLEIARMARDMMGGNGISDEFGVARHLVNLEVVNTYEG 371

Query: 396 TSEIRRMIIGREL 408
           T ++  +I+GR +
Sbjct: 372 THDVHALILGRAI 384


Lambda     K      H
   0.319    0.135    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: 346
Number of extensions: 22
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: 412
Length of database: 391
Length adjustment: 31
Effective length of query: 381
Effective length of database: 360
Effective search space:   137160
Effective search space used:   137160
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.

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