GapMind for catabolism of small carbon sources

 

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

Align Probable permease of ABC transporter, component of Amino acid transporter, PA5152-PA5155. Probably transports numerous amino acids including lysine, arginine, histidine, D-alanine and D-valine (Johnson et al. 2008). Regulated by ArgR (characterized)
to candidate 5210737 Shew_3165 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= TCDB::Q9HU30
         (231 letters)



>FitnessBrowser__PV4:5210737
          Length = 226

 Score =  105 bits (262), Expect = 7e-28
 Identities = 63/210 (30%), Positives = 110/210 (52%), Gaps = 12/210 (5%)

Query: 12  LLAGTWMTLKLSLAAVCVGLLLGLLGAIAKTSKYAALRFLGGTYTTIVRGVPETLWVLMI 71
           +L G  +TL ++L A+ +G +LG+   + K S    LR+    Y  ++RG P  + ++++
Sbjct: 24  ILNGLKVTLIVTLFAMILGAILGVATTLMKMSSRWYLRWPANLYVGVIRGTPVVVQLVIL 83

Query: 72  YFGTVSGLNALGDLFGKPDLALSPFAAGTLALGLCFGAYATEVFRGALLSIPRGHREAGQ 131
           YF  ++  +            +   +A  +A GL  GAY +E+ R  + ++ +G  EA +
Sbjct: 84  YFIVLATWD------------VDKVSAAIIAFGLNSGAYISEIIRAGIQAVDKGQTEAAR 131

Query: 132 ALGLSPGRIFWRIVLPQIWRVALPGLGNLYLILLKDTALVSLITLDEIMRKAQVASNATK 191
           +LGLS       ++LPQ  +  LP LGN +++LLK+TA++  I   ++MR  ++  + T 
Sbjct: 132 SLGLSQAVTMKEVILPQAIKNILPALGNEFIVLLKETAVIGFIGGVDLMRSGEIIRSRTF 191

Query: 192 EPFTFYMTAAAIYLSLTVVIMVALHFLERR 221
           E      T A IYL+LT      L   E+R
Sbjct: 192 EDSVPLFTCALIYLALTYSFTFMLSKFEKR 221


Lambda     K      H
   0.327    0.143    0.431 

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: 94
Number of extensions: 5
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: 231
Length of database: 226
Length adjustment: 23
Effective length of query: 208
Effective length of database: 203
Effective search space:    42224
Effective search space used:    42224
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: 46 (22.3 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