GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treV in Halomonas xinjiangensis TRM 0175

Align TreV, component of Trehalose porter (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= TCDB::Q97ZC0
         (324 letters)



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  245 bits (626), Expect = 1e-69
 Identities = 137/332 (41%), Positives = 206/332 (62%), Gaps = 22/332 (6%)

Query: 2   TVELIDIVKKYGKNI-VINGITEKIETGEFFVILGPSGEGKSTLLKILAGIEKLDKGKII 60
           +++L  + K Y  N+  + GI  +I  GEF V++GPSG GKSTLL+++AG+E +  G + 
Sbjct: 3   SIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGTLK 62

Query: 61  ADGADITDKPPEKRNVAMVFQNYALYPNMSVRDNIAFPLKMRGMKKEEIIERVEKAAKLL 120
            D   + D  P +R++AMVFQNYALYP+M+V  N+A+ LK RG+K+EEI  RV  AA +L
Sbjct: 63  IDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAAML 122

Query: 121 GISEILDKKVTQISGGQQQRVALARAIVRNPSYFLLDEPLSNLDARVRTTARGELKRIQK 180
            I   L++K  ++SGGQ+QRVA+ RA+VR PS FL DEPLSNLDA++R   R E+K++Q+
Sbjct: 123 EIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQLQR 182

Query: 181 ELKGTFIYVTHDQKEALSLADRIAILHKGKFEQVSDPKTLYEYPKTKWVAQFVGEFPMNF 240
            LK T +YVTHDQ EAL+L DR+ +L+ G  EQV  P  +YE P + +VA F+G   MN 
Sbjct: 183 RLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPAMNM 242

Query: 241 LPGELMKEKAQE------------IGFRPEWVEVGKGN-----LSCMVESVEASGESRYL 283
           LP   ++E+               IG RP+ + +   +     ++  VE  EA+G   +L
Sbjct: 243 LPVAYLRERGANGLLDHLAADTDVIGIRPDDLRIEAPDEDHLVVTGTVELFEAAGAESHL 302

Query: 284 ICNFKNNN----ITILSQEFYDVGQEVRFEII 311
             + + ++    I   ++     G+ +RF ++
Sbjct: 303 YVSLEGSDQPTVIRTSARPPVAEGETMRFHVL 334


Lambda     K      H
   0.318    0.137    0.385 

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: 256
Number of extensions: 7
Number of successful extensions: 1
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: 324
Length of database: 354
Length adjustment: 28
Effective length of query: 296
Effective length of database: 326
Effective search space:    96496
Effective search space used:    96496
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 (21.7 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