GapMind for catabolism of small carbon sources

 

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

Align Putrescine transport system permease protein PotI (characterized)
to candidate WP_011385764.1 AMB_RS17215 molybdate ABC transporter permease subunit

Query= SwissProt::P0AFL1
         (281 letters)



>NCBI__GCF_000009985.1:WP_011385764.1
          Length = 230

 Score = 83.2 bits (204), Expect = 5e-21
 Identities = 67/222 (30%), Positives = 108/222 (48%), Gaps = 11/222 (4%)

Query: 62  MSAVGLSLTIAACAATAAAILGTIAAVVLVRFGRFRGSNGFAFMITAPLVMPDVITGLSL 121
           M A+ LSL ++  A  A+  LG   A VL R   F G      +I  PLV+P V+ G  L
Sbjct: 9   MEALRLSLLVSFWAVAASLPLGLGCAWVLARLD-FPGKVVVDGIIHLPLVLPPVVVGYGL 67

Query: 122 LLLFVALAHAIGWPADRGMLTI---W----LAHVTFCTAYVAVVISSRLRELDRSIEEAA 174
           L++        GW  D   +T+   W    +A        +   I   L  +DR +E+AA
Sbjct: 68  LVVLGRRGVVGGWLYDWFGITLAFNWKGAAVASAVIAFPLMVRAIRLALEGVDRGLEQAA 127

Query: 175 MDLGATPLKVFFVITLPMIMPAIISGWLLAFTLSLDDL-VIASFVSG-PGAT-TLPMLVF 231
             LG  P++ F+ +TLP+++P +++G +LAF  SL +     +FVS  PG T TLP+ ++
Sbjct: 128 RTLGCGPIRTFWSVTLPLMLPGVLTGVILAFARSLSEFGATITFVSNIPGETRTLPIALY 187

Query: 232 SSVRMGVNPEINALATLILGAVGIVGFIAWYLMARAEKQRIR 273
           +  ++    E      +I   V     +A   +AR  + R++
Sbjct: 188 ALTQVPGGDEAALRLCVISVVVAFAALLASEYLARRVQARLK 229


Lambda     K      H
   0.330    0.140    0.430 

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: 173
Number of extensions: 12
Number of successful extensions: 4
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: 281
Length of database: 230
Length adjustment: 24
Effective length of query: 257
Effective length of database: 206
Effective search space:    52942
Effective search space used:    52942
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 (21.9 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