GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylH in Collimonas pratensis Ter91

Align D-xylose ABC transporter, permease protein (characterized)
to candidate WP_061938416.1 CPter91_RS06295 sugar ABC transporter permease

Query= CharProtDB::CH_024441
         (393 letters)



>NCBI__GCF_001584185.1:WP_061938416.1
          Length = 379

 Score =  389 bits (999), Expect = e-113
 Identities = 200/364 (54%), Positives = 262/364 (71%), Gaps = 2/364 (0%)

Query: 28  QVFVMIAAIIAIMLFFTWTTDGAYLSARNVSNLLRQTAITGILAVGMVFVIISAEIDLSV 87
           ++  ++ AI  I  FF+W T+G +++ RN+SNLLRQ +ITG+LA GMV VII+ EIDLSV
Sbjct: 14  KIMALLIAIALIWAFFSWKTEGGFVTPRNLSNLLRQMSITGVLACGMVLVIIAGEIDLSV 73

Query: 88  GSMMGLLGGVAAICDVWLGWPLPLTIIVTLVLGLLLGAWNGWWVAYRKVPSFIVTLAGML 147
           GSM+GLLGGVAA+ DV    PL L +++ L+ GL LG +NG+  AY ++PSFIV L GML
Sbjct: 74  GSMLGLLGGVAAVLDVTHHLPLSLNLLLVLLAGLALGLFNGYLTAYMRIPSFIVGLGGML 133

Query: 148 AFRGILIGITNGTTVSPTSAAMSQIGQSYLPASTGFIIGALGLMAF-VGWQWRGRMRRQA 206
           AFRGIL+G+T G T++P S+ M  +GQ YLP   G  +G +GL A  +   WR R  RQ 
Sbjct: 134 AFRGILLGVTGGLTIAPVSSEMVYLGQGYLPPQLGIALG-IGLFALALVLSWRRRSNRQQ 192

Query: 207 LGLQSPASTAVVGRQALTAIIVLGAIWLLNDYRGVPTPVLLLTLLLLGGMFMATRTAFGR 266
            GL  P+      R  L   ++L  +  LN Y G+P PVLLL  LL    ++ T+T FGR
Sbjct: 193 HGLPVPSVWRDAVRVLLIGAVLLAFVRTLNTYDGIPVPVLLLLALLGLFSYLTTQTVFGR 252

Query: 267 RIYAIGGNLEAARLSGINVERTKLAVFAINGLMVAIAGLILSSRLGAGSPSAGNIAELDA 326
           RIY++G N+EA RLSG+NV+  KL VF I G+M A+AGL+ ++RL AGSPSAGN+ ELDA
Sbjct: 253 RIYSVGSNMEATRLSGVNVQAVKLWVFGIMGVMCALAGLVNTARLAAGSPSAGNMGELDA 312

Query: 327 IAACVIGGTSLAGGVGSVAGAVMGAFIMASLDNGMSMMDVPTFWQYIVKGAILLLAVWMD 386
           IAAC IGGTS+ GG G+V GA++GA +MASLDNGMSM+DV T+WQ IVKG IL+LAVW+D
Sbjct: 313 IAACFIGGTSMRGGYGTVYGALIGALVMASLDNGMSMLDVDTYWQMIVKGGILMLAVWVD 372

Query: 387 SATK 390
            +T+
Sbjct: 373 VSTR 376


Lambda     K      H
   0.325    0.138    0.415 

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: 452
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: 393
Length of database: 379
Length adjustment: 30
Effective length of query: 363
Effective length of database: 349
Effective search space:   126687
Effective search space used:   126687
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 (21.6 bits)
S2: 50 (23.9 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