GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG in Skermanella stibiiresistens SB22

Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate WP_084164874.1 N825_RS19120 carbohydrate ABC transporter permease

Query= reanno::Smeli:SMc03063
         (380 letters)



>NCBI__GCF_000576635.1:WP_084164874.1
          Length = 288

 Score =  104 bits (260), Expect = 3e-27
 Identities = 71/230 (30%), Positives = 125/230 (54%), Gaps = 11/230 (4%)

Query: 151 LDNYAEVLSAAGIGRSFLNSLTVAVPSTVIPILIAAFAAYALAWMPFPGRAVL-LAVVVG 209
           LDNY EVL    +  S  NS+ +AV +T++ + +   AAYALA   F  +  L    +  
Sbjct: 68  LDNYFEVLFNRDVLSSLTNSIIIAVSTTILAVGLGTPAAYALARFEFKSKEELWFWFITN 127

Query: 210 LLVVPLQMSLIPLLQLYNGVGAFFGVSAKTYMGIWLAHTGFGLPLAIYLLRNYMAGLPRE 269
            ++ P+ ++L P+  +   +         T++ + L +  F LP+ +++  +   G+P++
Sbjct: 128 RMLSPIVVAL-PIFLMARTLNLI-----DTHIVLILVYLTFNLPIVVWICTDQFRGVPKD 181

Query: 270 IMESARVDGASDFDIFVKIILPLSFPALASFAIFQFLWTWNDLLVAIVFLGAGDDKLVLT 329
           + E+AR+ GAS F IF +I LPL+ P +A  AIF F+++WN+LL A+V     +      
Sbjct: 182 LDEAARLAGASRFTIFWRIALPLAMPGVAVSAIFSFIFSWNELLYALVL--TRNVARTAP 239

Query: 330 GRLVNLLGSRGGNWEILTASAFITIVVPLIVF-FALQRYLVRGLLAGSVK 378
               + +      W  + A+  + IV+P+IVF   + ++LV+GL  G+VK
Sbjct: 240 VAATSFMSGYDLPWGEIMATGTL-IVLPVIVFALIVSKHLVQGLTMGAVK 288


Lambda     K      H
   0.324    0.139    0.418 

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: 243
Number of extensions: 14
Number of successful extensions: 3
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: 380
Length of database: 288
Length adjustment: 28
Effective length of query: 352
Effective length of database: 260
Effective search space:    91520
Effective search space used:    91520
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Sep 24 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