GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Pf6N2E2_5404 in Shewanella loihica PV-4

Align ABC transporter for D-Alanine, permease component 1 (characterized)
to candidate 5210737 Shew_3165 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= reanno::pseudo6_N2E2:Pf6N2E2_5404
         (365 letters)



>FitnessBrowser__PV4:5210737
          Length = 226

 Score = 96.3 bits (238), Expect = 7e-25
 Identities = 63/203 (31%), Positives = 111/203 (54%), Gaps = 7/203 (3%)

Query: 157 GLMLTLVIATVGIVGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVPLITVLFMSSVM 216
           GL +TL++    ++    LG+   L + S+   +R     ++   RG P++  L    V+
Sbjct: 27  GLKVTLIVTLFAMILGAILGVATTLMKMSSRWYLRWPANLYVGVIRGTPVVVQL----VI 82

Query: 217 LPLFLPEGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQYEAAAAMGLGYWRSMG 276
           L   +    + DK+  A+I   L   AYI+E++R G+QA+ KGQ EAA ++GL    +M 
Sbjct: 83  LYFIVLATWDVDKVSAAIIAFGLNSGAYISEIIRAGIQAVDKGQTEAARSLGLSQAVTMK 142

Query: 277 LVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNS--VKQAAADPKWLGMATEGY 334
            VILPQA+K ++P + N FI L K+T+++  IG  DL+ S  + ++      + + T   
Sbjct: 143 EVILPQAIKNILPALGNEFIVLLKETAVIGFIGGVDLMRSGEIIRSRTFEDSVPLFTCAL 202

Query: 335 VFAALVFWIFCFGMSRYSMHLER 357
           ++ AL +  F F +S++   L++
Sbjct: 203 IYLALTY-SFTFMLSKFEKRLKQ 224


Lambda     K      H
   0.330    0.144    0.469 

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: 251
Number of extensions: 14
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: 365
Length of database: 226
Length adjustment: 26
Effective length of query: 339
Effective length of database: 200
Effective search space:    67800
Effective search space used:    67800
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.

Links

Downloads

Related tools

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