GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylF in Cronobacter condimenti 1330

Align D-xylose ABC transporter, periplasmic D-xylose-binding protein (characterized)
to candidate WP_007680677.1 BN137_RS01920 D-xylose ABC transporter substrate-binding protein

Query= CharProtDB::CH_003787
         (330 letters)



>NCBI__GCF_000319285.1:WP_007680677.1
          Length = 330

 Score =  574 bits (1479), Expect = e-168
 Identities = 289/330 (87%), Positives = 314/330 (95%)

Query: 1   MKIKNILLTLCTSLLLTNVAAHAKEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFV 60
           MKIK ++LTLC SL+LT+ +  AK+VKIGMAIDDLRLERWQKDRDIFV KAESLGAKVFV
Sbjct: 1   MKIKQLILTLCASLVLTSFSGIAKDVKIGMAIDDLRLERWQKDRDIFVSKAESLGAKVFV 60

Query: 61  QSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDAD 120
           QSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNV+ EAK+EGIKVLAYDRMIN+AD
Sbjct: 61  QSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVIAEAKREGIKVLAYDRMINNAD 120

Query: 121 IDFYISFDNEKVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGK 180
           IDFYISFDNEKVGE+QA++LVD VPQGNYFLMGGSPVDNNA+LFR GQMKVLKP++DSGK
Sbjct: 121 IDFYISFDNEKVGEIQAQSLVDNVPQGNYFLMGGSPVDNNARLFRDGQMKVLKPFIDSGK 180

Query: 181 IKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVA 240
           IKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGL+ KVA
Sbjct: 181 IKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLASKVA 240

Query: 241 ISGQDADLAGIKRIAAGTQTMTVYKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDV 300
           ISGQDADLAGIKRI AGTQTMTVYKPIT LANTAAE+AVELGN ++PK+D TLNNGLKDV
Sbjct: 241 ISGQDADLAGIKRIMAGTQTMTVYKPITQLANTAAEVAVELGNDKQPKSDATLNNGLKDV 300

Query: 301 PSRLLTPIDVNKNNIKDTVIKDGFHKESEL 330
           PSRLLTPI V+K+NI+ TVIKDGFHK+S+L
Sbjct: 301 PSRLLTPIKVDKSNIESTVIKDGFHKKSDL 330


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: 483
Number of extensions: 7
Number of successful extensions: 1
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: 330
Length adjustment: 28
Effective length of query: 302
Effective length of database: 302
Effective search space:    91204
Effective search space used:    91204
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 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