GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Snodgrassella alvi wkB2

Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate WP_025331514.1 SALWKB2_RS09875 ABC transporter ATP-binding protein

Query= TCDB::Q88P35
         (384 letters)



>NCBI__GCF_000600005.1:WP_025331514.1
          Length = 311

 Score =  150 bits (379), Expect = 5e-41
 Identities = 80/234 (34%), Positives = 134/234 (57%), Gaps = 2/234 (0%)

Query: 4   LELRNVNKTYGSGLPDTLKDIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGGAIL 63
           L  + +NK +   +     D+ L + DG+ + ++G SG GKSTL+N  AGL Q   G I 
Sbjct: 2   LSWQQINKKFSDKV--VAADLSLEVADGQLVAVLGESGSGKSTLLNMAAGLVQPDSGNIF 59

Query: 64  IDEQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVAKLL 123
           I+E++++ + P+ R I ++FQ YAL P ++V +N+ FGL++ ++ +     +  ++   +
Sbjct: 60  INEENITFLLPEQRRIGLMFQDYALLPHLNVWQNVAFGLRMHRVSKPQAQHQAMQMLAEV 119

Query: 124 QIEHLLARKPAQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183
            +    AR+   LSGG+QQRVA+ RAL  +P+  L DEP S LD  LR  ++     + +
Sbjct: 120 GLSEAAARQVDVLSGGEQQRVALARALVLQPQALLLDEPFSALDTTLRASLQQLTVRLLR 179

Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANQFVASFIG 237
           + K   V VTH  +EA  L D++ +++ G   Q GT  Q+   PA+ + A  +G
Sbjct: 180 QQKCPAVLVTHSPLEAFALADRICLLRHGRWIQQGTAAQLLARPADAWAARLLG 233


Lambda     K      H
   0.320    0.137    0.391 

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: 259
Number of extensions: 11
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: 384
Length of database: 311
Length adjustment: 29
Effective length of query: 355
Effective length of database: 282
Effective search space:   100110
Effective search space used:   100110
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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