GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Mannitol, D-Mannose, and D-Mannose, ATPase component (characterized)
to candidate WP_011383734.1 AMB_RS06730 nitrate ABC transporter ATP-binding protein

Query= reanno::pseudo13_GW456_L13:PfGW456L13_3039
         (367 letters)



>NCBI__GCF_000009985.1:WP_011383734.1
          Length = 452

 Score =  148 bits (373), Expect = 3e-40
 Identities = 81/195 (41%), Positives = 127/195 (65%), Gaps = 6/195 (3%)

Query: 17  SIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSGGTIELDGRDITEVSPAKRD 76
           ++++G+D ++ + E V  +G SG GKSTLLR++AGL + +GG ++  G  +T   PAK  
Sbjct: 29  TVLEGVDFKLEEGEIVALLGKSGSGKSTLLRIMAGLIKANGGEVKYRGHLMT--GPAK-G 85

Query: 77  LAMVFQTYALYPHMSVRKNMSFALDLAGVAKAEVEKKVSEAARILELGPMLERKPKQLSG 136
           ++MVFQ++AL+P ++V +N+   L+ AGVAKAE E++ +EA  ++ LG      PK+LSG
Sbjct: 86  ISMVFQSFALFPWLTVEENVELGLEAAGVAKAEREERANEAIDLIGLGGYESAYPKELSG 145

Query: 137 GQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELLRLHKELQAT---MIYVTHD 193
           G RQRV   RA+V  P + L DEP S LD      +R +LL L  E +     ++ V+H+
Sbjct: 146 GMRQRVGFARALVMRPDVLLLDEPFSALDVLTSETLREDLLELWDERKIPTKGILLVSHN 205

Query: 194 QVEAMTMADKVVVLN 208
             EA++MAD+V+V +
Sbjct: 206 IEEAVSMADRVLVFS 220


Lambda     K      H
   0.320    0.137    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: 356
Number of extensions: 17
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 367
Length of database: 452
Length adjustment: 31
Effective length of query: 336
Effective length of database: 421
Effective search space:   141456
Effective search space used:   141456
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 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