GapMind for catabolism of small carbon sources

 

Alignments for a candidate for liuC in Magnetospirillum magneticum AMB-1

Align methylglutaconyl-CoA hydratase (EC 4.2.1.18) (characterized)
to candidate WP_011384978.1 AMB_RS13070 enoyl-CoA hydratase

Query= BRENDA::F4JML5
         (301 letters)



>NCBI__GCF_000009985.1:WP_011384978.1
          Length = 256

 Score =  155 bits (392), Expect = 9e-43
 Identities = 87/246 (35%), Positives = 139/246 (56%), Gaps = 3/246 (1%)

Query: 55  IIEVNLDRPVTKNAINKEMLKSLQNAFESIHQDNSARVVMIRSLVPGVFCAGADLKERRT 114
           ++ + ++RP  KNA+N E+ + L     ++  D S R +++       F AGAD+K+   
Sbjct: 13  VVLLRINRPDAKNALNGEVRRLLAEHMTTLGADPSVRAIVMTGNQEA-FAAGADIKDMAE 71

Query: 115 MSPSEVHTYVNSLRYMFSFIEALSIPTIAAIEGAALGGGLEMALACDLRICGENAVFGLP 174
           +   E+    N L  ++  I     P IAA+ G A GGG E+ +  D+ + GENA F  P
Sbjct: 72  VGAIELMQRNNHL--LWRAIANCPKPVIAAVNGYAWGGGCELVMHADIIVAGENASFSQP 129

Query: 175 ETGLAIIPGAGGTQRLSRLVGRSVSKELIFTGRKIDAIEAANKGLVNICVTAGEAHEKAI 234
           E  + I+PGAGGTQRL+R VG+  +  ++ TG+ I  +EA   GL ++ V   E  +KA+
Sbjct: 130 EVKVGIMPGAGGTQRLTRAVGKFKAMLMVMTGQAISGVEAGQMGLASVVVPDAEVVDKAL 189

Query: 235 EMAQQINEKGPLAIKMAKKAIDEGIETNMASGLEVEEMCYQKLLNTQDRLEGLAAFAEKR 294
           E+A+ I+   P+AI   K+ +  G + ++ + L +E   +Q L  + D+ EG+ AF EKR
Sbjct: 190 EIAKTISRMPPVAIAQIKEVLLAGQDASLDTALMLERKAFQLLFASADQKEGMKAFIEKR 249

Query: 295 KPLYTG 300
           KP Y G
Sbjct: 250 KPTYQG 255


Lambda     K      H
   0.318    0.134    0.373 

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: 148
Number of extensions: 6
Number of successful extensions: 2
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: 301
Length of database: 256
Length adjustment: 25
Effective length of query: 276
Effective length of database: 231
Effective search space:    63756
Effective search space used:    63756
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: 47 (22.7 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