GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylGsa in Snodgrassella alvi wkB2

Align Xylose/arabinose import ATP-binding protein XylG; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_025329798.1 SALWKB2_RS00760 amino acid ABC transporter ATP-binding protein

Query= uniprot:P0DTT6
         (251 letters)



>NCBI__GCF_000600005.1:WP_025329798.1
          Length = 242

 Score =  113 bits (282), Expect = 4e-30
 Identities = 69/226 (30%), Positives = 129/226 (57%), Gaps = 6/226 (2%)

Query: 4   LLEIRDVHKSFGAVKALDGVSMEINKGEVVALLGDNGAGKSTLIKIISGYHKPDRGDLVF 63
           ++E ++VHK F  +  ++GV++ +++GEVV + G +G+GKSTLI+ ++   K  +G++  
Sbjct: 1   MIEFKNVHKWFKDLHVINGVNLTVSQGEVVVVCGPSGSGKSTLIRTVNQLEKIQQGEIWV 60

Query: 64  EGKKVIFNSPNDARSLGIET--IYQDLALIPDLPIYYNIFLAREVTNKIFLNKKKMMEES 121
           +G  V  +   D   +  E   ++Q   L P L +  NI L+     K   ++ +   ++
Sbjct: 61  DGINVA-DPKADLNRVRTEVGFVFQHFNLYPHLTVLENIILSPMKVKKE--SRAQAEAKA 117

Query: 122 KKLLDSLQIRIPDINMKVENLSGGQRQAVAVARAVYFSAKMILMDEPTAALSVVEARKVL 181
           K+LL  + +     +   + LSGGQ+Q VA+AR +    +++L DEPT+AL      +VL
Sbjct: 118 KELLAKVGLA-HKCDAFPQQLSGGQQQRVAIARGLAMEPRVMLFDEPTSALDPEMIGEVL 176

Query: 182 ELARNLKKKGLGVLIITHNIIQGYEVADRIYVLDRGKIIFHKKKEE 227
           ++ ++L   G+ ++++TH +    EVADR+  +D G+I+     EE
Sbjct: 177 KVMKDLALSGMTMMVVTHEMGFAREVADRVVFIDHGEIVEEATPEE 222


Lambda     K      H
   0.318    0.137    0.371 

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: 112
Number of extensions: 3
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: 251
Length of database: 242
Length adjustment: 24
Effective length of query: 227
Effective length of database: 218
Effective search space:    49486
Effective search space used:    49486
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: 41 (21.7 bits)
S2: 46 (22.3 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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