GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Marivita geojedonensis DPG-138

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_085638943.1 MGEO_RS13990 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_002115805.1:WP_085638943.1
          Length = 350

 Score =  290 bits (743), Expect = 3e-83
 Identities = 159/363 (43%), Positives = 220/363 (60%), Gaps = 18/363 (4%)

Query: 1   MGQIQLTDLTKRFGDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGDI 60
           M  + L  + KR+G T  +  + LD+ D EF V VGPSGCGKST LRM+AGLE  T G I
Sbjct: 1   MSGVTLESVIKRYGQTQVIHGVDLDVQDGEFCVFVGPSGCGKSTLLRMVAGLEETTEGTI 60

Query: 61  YIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVAE 120
            IGG  +    P +R ++MVFQ YALYPHMTV +N+ FGL+   G+ + +  E+V E + 
Sbjct: 61  RIGGRDVTRLDPSDRGVSMVFQTYALYPHMTVEENMGFGLKMT-GHAAKDIKEKVAEASR 119

Query: 121 TLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQNL 180
            L + D L RKP  LSGGQ+QRVA+GRAIVR PEVFL DEPLSNLDA+LR EMR E+  L
Sbjct: 120 ILKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVEMRVEIARL 179

Query: 181 QDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPMI 240
             ++  T +YVTH+Q EAMT+AD+I V+  G ++QV +P E Y +P+N FVA FIG P +
Sbjct: 180 HKEIGATMIYVTHDQVEAMTLADKIVVLRAGRIEQVGAPMELYRDPDNRFVAGFIGSPSM 239

Query: 241 NLVRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAALDDHD 300
           N +RG       V +   + + +    S  +  + ++G+RPE +E+   +          
Sbjct: 240 NFIRGRVQGGEVVSDGLVHSVSKTA--SAQEGQEVLIGLRPEHLELRPGSSH-------- 289

Query: 301 LQMDVTVVEPHGDQNVLHLSHPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDKIHLFD 360
            ++D+T  E  G  +  HL  PD     + +     G H  + GD V + + PD + LFD
Sbjct: 290 -RVDLT--ESLGGVSYAHLIGPD----GEKIIVEERGDHRSSDGDMVDLVVDPDHMFLFD 342

Query: 361 AET 363
           A+T
Sbjct: 343 AKT 345


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: 346
Number of extensions: 15
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: 350
Length adjustment: 30
Effective length of query: 353
Effective length of database: 320
Effective search space:   112960
Effective search space used:   112960
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.

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