GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Dethiosulfovibrio salsuginis USBA 82

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085544777.1 B9Y55_RS07660 ABC transporter ATP-binding protein

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_900177735.1:WP_085544777.1
          Length = 351

 Score =  239 bits (610), Expect = 9e-68
 Identities = 122/266 (45%), Positives = 178/266 (66%), Gaps = 9/266 (3%)

Query: 3   QIQLTDLTKRF----GDTV--AVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPT 56
           ++++++++K F    G  V  AVD ++L + D E + L+GPSGCGK+T LRM+AG E P+
Sbjct: 2   ELRISEVSKVFPSHDGGAVVRAVDSVNLTVADGELVTLLGPSGCGKTTLLRMIAGFEDPS 61

Query: 57  SGDIYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVV 116
            GD+Y G   +N   P  R+  +VFQ YA++PH+ V +NI FGL  + G    +   ++ 
Sbjct: 62  EGDLYFGDRRVNNVAPNRRNATLVFQSYAIFPHLNVFENIAFGLRLK-GLKEGDIRSKME 120

Query: 117 EVAETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTE 176
           +V   +G+  +  R+P +LSGGQQQRVAL RA+V +PE+ L DEPLSNLDAKLR +MR +
Sbjct: 121 KVVHMVGLGGMETRRPSQLSGGQQQRVALARAVVMEPELLLFDEPLSNLDAKLREQMRID 180

Query: 177 LQNLQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIG 236
           ++ LQ  L +T+VYVTH+Q EAM+++DR+ VM DG ++Q  SP + Y  P N FVA+FIG
Sbjct: 181 IRRLQKALGITSVYVTHDQAEAMSISDRVVVMKDGRIEQSGSPVDLYARPRNRFVADFIG 240

Query: 237 EPMINLVRGTRSESTFVGEHFSYPLD 262
           +   N + GT SE   +    SYP+D
Sbjct: 241 K--ANFLDGTASEGGVILGGKSYPMD 264


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: 324
Number of extensions: 14
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: 383
Length of database: 351
Length adjustment: 30
Effective length of query: 353
Effective length of database: 321
Effective search space:   113313
Effective search space used:   113313
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: 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