GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Phaeacidiphilus oryzae TH49

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_000744815.1:WP_037573817.1
          Length = 369

 Score =  290 bits (743), Expect = 3e-83
 Identities = 173/353 (49%), Positives = 221/353 (62%), Gaps = 6/353 (1%)

Query: 14  GDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDIYIGGDHMNYRVPQ 73
           GD  AVD L L+I D EFLVLVGPSGCGKST+LRMLAGLE   +G I IG   + +  P+
Sbjct: 16  GDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNGAIRIGERDVTHLPPK 75

Query: 74  NRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAETLGIADLLDRKPD 133
           +RDIAMVFQ+YALYPHMTV  N+ F L+   G   AE   +V E A+ L + + LDRKP 
Sbjct: 76  DRDIAMVFQNYALYPHMTVADNMGFALKIA-GVNKAEIRSKVEEAAKILDLTEFLDRKPK 134

Query: 134 ELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNLQDQLAVTTVYVTH 193
            LSGGQ+QRVA+GRAIVR+P+VFLMDEPLSNLDAKLR   RT++  LQ +L +TTVYVTH
Sbjct: 135 ALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAGLQRRLGITTVYVTH 194

Query: 194 NQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMINLVRGTRSE-STF 252
           +Q EAMTM DR+AV+ DG LQQV +P   Y  P NLFVA FIG P +NLV    ++    
Sbjct: 195 DQVEAMTMGDRVAVLKDGLLQQVDTPRNMYDRPANLFVAGFIGSPAMNLVEVPITDGGVK 254

Query: 253 VGEHFSYPLDEDVMESVDDRDDFV-LGVRPEDIEVADAAPDDAALDDHDLQMDVTVVEPH 311
            GE       + V E+ +  D  V +GVRPE +++      +   +D  L + V VVE  
Sbjct: 255 FGESVVQVSRDAVGEAANAGDKTVTVGVRPEHLDIVGGT--EGGGEDKGLAVTVNVVEEL 312

Query: 312 GDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDKIHLFDAETG 364
           G    ++ S        D +  V  G  +  +GD++ V     + H+F   TG
Sbjct: 313 GADGYVYGSAKVGTETIDLVVRV-GGRDIPMKGDQLRVVPRAGETHVFSTSTG 364


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: 399
Number of extensions: 20
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: 369
Length adjustment: 30
Effective length of query: 353
Effective length of database: 339
Effective search space:   119667
Effective search space used:   119667
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: 50 (23.9 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