GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Rhizorhabdus wittichii RW1

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_000016765.1:WP_012048833.1
          Length = 241

 Score =  143 bits (360), Expect = 6e-39
 Identities = 88/240 (36%), Positives = 133/240 (55%), Gaps = 9/240 (3%)

Query: 4   IQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIG 63
           I +  + K +G   A+ ++SLD+   E +V+ GPSG GKST +R + GLET   G I IG
Sbjct: 2   IHMAGVGKWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIG 61

Query: 64  GDHM--NYRVPQN--RDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVA 119
            D +  + RV Q     + MVFQD+ L+PH+T+ +N      +  G      +    E+ 
Sbjct: 62  EDEVRPDRRVLQRIRARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELL 121

Query: 120 ETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQN 179
           E + IAD  D+ P +LSGGQQQR A+ RA+   PE+ L DEP S LDA++  E+   ++ 
Sbjct: 122 ERVRIADQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIMKA 181

Query: 180 LQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECY----HEPNNLFVAEFI 235
           L  +  +T + VTH    A  +ADRI  MD G++ +  SP + +    HE    F++  +
Sbjct: 182 LATE-GITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRAFLSRLL 240


Lambda     K      H
   0.317    0.135    0.386 

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: 210
Number of extensions: 7
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: 383
Length of database: 241
Length adjustment: 27
Effective length of query: 356
Effective length of database: 214
Effective search space:    76184
Effective search space used:    76184
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 (21.6 bits)
S2: 48 (23.1 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