GapMind for catabolism of small carbon sources

 

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

Align putrescine transport system permease protein PotH (characterized)
to candidate WP_083763520.1 AMB_RS13200 putrescine ABC transporter permease PotH

Query= CharProtDB::CH_088338
         (317 letters)



>NCBI__GCF_000009985.1:WP_083763520.1
          Length = 316

 Score =  339 bits (870), Expect = 5e-98
 Identities = 172/289 (59%), Positives = 214/289 (74%), Gaps = 2/289 (0%)

Query: 23  LQMKHGRKLVIALPYIWLILLFLLPFLIVFKISLAEMARAIPPYTELMEWADGQLSITLN 82
           L+ + GR LV   PY WL+L FL+PFLIV KISL+E    IPPY  L++WA+G    TL 
Sbjct: 24  LEGRGGRFLVGLAPYAWLLLFFLVPFLIVLKISLSEPQMGIPPYMPLIDWAEGAFKGTL- 82

Query: 83  LGNFLQLTDDPLYFDAYLQSLQVAAISTFCCLLIGYPLAWAVAHSKPSTRNILLLLVILP 142
              +  L  D LY  AYL SL++A IST  CLL+GYP A+A+A +  S R  LL+LV LP
Sbjct: 83  -AGYNTLLGDNLYLLAYLGSLKLAGISTLGCLLLGYPAAYAIARAPQSRRQALLMLVALP 141

Query: 143 SWTSFLIRVYAWMGILKNNGVLNNFLLWLGVIDQPLTILHTNLAVYIGIVYAYVPFMVLP 202
            WTSFLIRVYAW+GILKN G+LN  L  LG+I +PL IL T+ AV IG+VY+Y+PFM+LP
Sbjct: 142 FWTSFLIRVYAWIGILKNEGLLNMALQALGLISEPLQILETSTAVVIGMVYSYLPFMILP 201

Query: 203 IYTALIRIDYSLVEAALDLGARPLKTFFTVIVPLTKGGIIAGSMLVFIPAVGEFVIPELL 262
           +Y  L ++D SL+EAA DLG RP K F  V +PL+  G+IAG MLVFIPAVGEFVIP+LL
Sbjct: 202 LYATLEKMDLSLLEAAADLGCRPFKAFLAVTLPLSMPGVIAGCMLVFIPAVGEFVIPDLL 261

Query: 263 GGPDSIMIGRVLWQEFFNNRDWPVASAVAIIMLLLLIVPIMWFHKHQQK 311
           GGPD+++IG+VLW EFF+NRDWP ASAVA+ ML+LL+VPIM F   + K
Sbjct: 262 GGPDTLVIGKVLWAEFFDNRDWPTASAVAVAMLVLLVVPIMVFQHFEAK 310


Lambda     K      H
   0.328    0.144    0.457 

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: 375
Number of extensions: 15
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: 317
Length of database: 316
Length adjustment: 27
Effective length of query: 290
Effective length of database: 289
Effective search space:    83810
Effective search space used:    83810
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 48 (23.1 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