GapMind for catabolism of small carbon sources

 

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

Align BadK (characterized)
to candidate WP_011382625.1 AMB_RS00905 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase

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



>NCBI__GCF_000009985.1:WP_011382625.1
          Length = 261

 Score =  152 bits (384), Expect = 7e-42
 Identities = 99/261 (37%), Positives = 143/261 (54%), Gaps = 6/261 (2%)

Query: 3   SNPILTETQGRVGIITLNRPDVLNALNDALMDALGGALLAFDADDGIGAIVIAGNTRAFA 62
           S  IL    G V  ITLNRP  +NA N  +  AL  A+ A  A+DG   +VI G  + F 
Sbjct: 2   SETILVARTGDVTTITLNRPGRINAFNVEMHGALRSAV-AHAAEDGTRCLVITGAGKGFC 60

Query: 63  AGADIASMAAWSYSDV--YGSNFITRNWETIRQIRK---PVLAAVAGLAYGGGCELALAC 117
           AG D++   +         G++   R    IR ++    PV+AAV G A G G  LALAC
Sbjct: 61  AGQDLSDRVSKPGDPPPDLGASLDARYNPLIRSLKALPMPVIAAVNGTAAGAGANLALAC 120

Query: 118 DIVIAGRSAKFALPEIKLGLLPGAGGTQRLPRAIGKAKAMDMCLSARPLNAEEADRYGLV 177
           DIV+A RSA F     K+GL+P +GGT  LPR +G A+A  + +    + AE+A ++G++
Sbjct: 121 DIVVAARSAAFVQSFCKVGLIPDSGGTWTLPRLVGTARATALMMLGEKVTAEQAMQWGMI 180

Query: 178 SRVVDDDRLRDETVALATTIAAFSAPALMALKESLNRAFESTLAEGILFERRELHARFAS 237
            R VDD++L    +A+A  +AA     L  +K++L R+  +TL   +  ER        +
Sbjct: 181 WRCVDDEQLLPTVLAMAAQLAAQPTRGLALMKKALARSGANTLDAQLDLERDLQTEAGCT 240

Query: 238 ADAREGIQAFLEKRAPCFSHR 258
            D +EG++AF+EKR P F  R
Sbjct: 241 QDYQEGVRAFMEKRPPRFEGR 261


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: 131
Number of extensions: 4
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: 261
Length adjustment: 24
Effective length of query: 234
Effective length of database: 237
Effective search space:    55458
Effective search space used:    55458
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