GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xacJ in Halomonas xinjiangensis TRM 0175

Align Xylose/arabinose import ATP-binding protein XacJ; EC 7.5.2.13 (characterized, see rationale)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= uniprot:D4GP38
         (383 letters)



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  268 bits (686), Expect = 1e-76
 Identities = 160/367 (43%), Positives = 225/367 (61%), Gaps = 24/367 (6%)

Query: 1   MGQIQLTDLTKRF-GDTVAVDDLSLDIDDEEFLVLVGPSGCGKSTTLRMLAGLETPTSGD 59
           M  IQLT L K + G+  AV  + L+I D EF+VLVGPSGCGKST LRM+AGLET T G 
Sbjct: 1   MASIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGT 60

Query: 60  IYIGGDHMNYRVPQNRDIAMVFQDYALYPHMTVRQNIRFGLEEEEGYTSAERDERVVEVA 119
           + I    +N   P  RDIAMVFQ+YALYPHMTV  N+ +GL+   G    E + RV + A
Sbjct: 61  LKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNR-GVKREEIERRVHDAA 119

Query: 120 ETLGIADLLDRKPDELSGGQQQRVALGRAIVRDPEVFLMDEPLSNLDAKLRAEMRTELQN 179
             L I   L+RKP +LSGGQ+QRVA+GRA+VR+P  FL DEPLSNLDAKLR +MR E++ 
Sbjct: 120 AMLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQ 179

Query: 180 LQDQLAVTTVYVTHNQTEAMTMADRIAVMDDGELQQVASPFECYHEPNNLFVAEFIGEPM 239
           LQ +L  T++YVTH+Q EA+T+ DR+ V++ G ++QV +P E Y +P ++FVA FIG P 
Sbjct: 180 LQRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPA 239

Query: 240 INLVRGTRSESTFVGEHFSYPLDEDVMESVDDRDDFVLGVRPEDIEVADAAPDDAALDDH 299
           +N++        ++ E  +  L + +    D     V+G+RP+D+ +   APD+   D  
Sbjct: 240 MNML-----PVAYLRERGANGLLDHLAADTD-----VIGIRPDDLRI--EAPDE---DHL 284

Query: 300 DLQMDVTVVEPHGDQNVLHLS--HPDQPSADDALQAVTEGMHLVTRGDRVTVTIPPDKIH 357
            +   V + E  G ++ L++S    DQP+        T     V  G+ +   + P  +H
Sbjct: 285 VVTGTVELFEAAGAESHLYVSLEGSDQPTV-----IRTSARPPVAEGETMRFHVLPSALH 339

Query: 358 LFDAETG 364
            F+  +G
Sbjct: 340 PFNQASG 346


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: 342
Number of extensions: 14
Number of successful extensions: 4
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: 354
Length adjustment: 30
Effective length of query: 353
Effective length of database: 324
Effective search space:   114372
Effective search space used:   114372
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