GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylF in Tistlia consotensis USBA 355

Align D-xylose ABC transporter, periplasmic D-xylose-binding protein (characterized)
to candidate WP_085126662.1 B9O00_RS29725 D-xylose ABC transporter substrate-binding protein

Query= CharProtDB::CH_003787
         (330 letters)



>NCBI__GCF_900177295.1:WP_085126662.1
          Length = 345

 Score =  246 bits (628), Expect = 6e-70
 Identities = 136/321 (42%), Positives = 194/321 (60%), Gaps = 9/321 (2%)

Query: 15  LLTNVAAHAKEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQI 74
           L + +A  A  + +G++  + + ERW+ D        E  GA+     A  +   Q+S +
Sbjct: 16  LSSTLALAADPLIVGVSWSNFQEERWKTDEAAIKAALEKAGARYISTDAQSSSAKQLSDV 75

Query: 75  ENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNEKVGE 134
           E++I+RG + L+I+  +   +   +  A  EGI V+ YDR+I D    FY++FDN++VG 
Sbjct: 76  ESLISRGANALIILAQDAAAIGPAINAADAEGIPVVGYDRLIEDPRA-FYLTFDNKEVGR 134

Query: 135 LQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVDGWLP 194
           +QA+A+ D  P+GNY  + GSP D NA    +GQM+VLKP +D G IKVVG Q+ DGWLP
Sbjct: 135 MQAQAVYDKQPKGNYVFILGSPTDPNADFLFSGQMEVLKPAIDKGDIKVVGKQYTDGWLP 194

Query: 195 ENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRI 254
            NA + ME  LTA NNK+DAVVASND TAGG + AL+AQG+ G + +SGQD D A + R+
Sbjct: 195 ANAQRNMEQILTATNNKVDAVVASNDGTAGGVVAALTAQGMQG-IPVSGQDGDHAALNRV 253

Query: 255 AAGTQTMTVYKPITLLANTAAEIAVELGNGQ-----EPKADTTLNNGLKDVPSRLLTPID 309
           A GTQT++V+K    L   AAEIAV L  G+     E     T  NG K + S+ L P+ 
Sbjct: 254 ALGTQTVSVWKDARALGKRAAEIAVALAKGKKLSEIEGAESWTSPNG-KTLSSQFLKPVP 312

Query: 310 VNKNNIKDTVIKDGFHKESEL 330
           + + N+ D VI  G+    E+
Sbjct: 313 ITRKNL-DVVIDAGWITRQEV 332


Lambda     K      H
   0.314    0.132    0.366 

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: 279
Number of extensions: 10
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: 330
Length of database: 345
Length adjustment: 28
Effective length of query: 302
Effective length of database: 317
Effective search space:    95734
Effective search space used:    95734
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)

This GapMind analysis is from Apr 09 2024. 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