GapMind for catabolism of small carbon sources

 

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

Align BadK (characterized)
to candidate WP_011384978.1 AMB_RS13070 enoyl-CoA hydratase

Query= metacyc::MONOMER-943
         (258 letters)



>NCBI__GCF_000009985.1:WP_011384978.1
          Length = 256

 Score =  192 bits (489), Expect = 4e-54
 Identities = 105/246 (42%), Positives = 150/246 (60%), Gaps = 9/246 (3%)

Query: 14  VGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFAAGADIASMAAW 73
           V ++ +NRPD  NALN  +   L   +    AD  + AIV+ GN  AFAAGADI  MA  
Sbjct: 13  VVLLRINRPDAKNALNGEVRRLLAEHMTTLGADPSVRAIVMTGNQEAFAAGADIKDMA-- 70

Query: 74  SYSDVYGSNFITRN----WETIRQIRKPVLAAVAGLAYGGGCELALACDIVIAGRSAKFA 129
              +V     + RN    W  I    KPV+AAV G A+GGGCEL +  DI++AG +A F+
Sbjct: 71  ---EVGAIELMQRNNHLLWRAIANCPKPVIAAVNGYAWGGGCELVMHADIIVAGENASFS 127

Query: 130 LPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLVSRVVDDDRLRDE 189
            PE+K+G++PGAGGTQRL RA+GK KAM M ++ + ++  EA + GL S VV D  + D+
Sbjct: 128 QPEVKVGIMPGAGGTQRLTRAVGKFKAMLMVMTGQAISGVEAGQMGLASVVVPDAEVVDK 187

Query: 190 TVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFASADAREGIQAFLE 249
            + +A TI+     A+  +KE L    +++L   ++ ER+     FASAD +EG++AF+E
Sbjct: 188 ALEIAKTISRMPPVAIAQIKEVLLAGQDASLDTALMLERKAFQLLFASADQKEGMKAFIE 247

Query: 250 KRAPCF 255
           KR P +
Sbjct: 248 KRKPTY 253


Lambda     K      H
   0.321    0.135    0.389 

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: 119
Number of extensions: 3
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: 258
Length of database: 256
Length adjustment: 24
Effective length of query: 234
Effective length of database: 232
Effective search space:    54288
Effective search space used:    54288
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 (21.9 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