GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SMc04256 in Halomonas xinjiangensis TRM 0175

Align ABC transporter for D-Cellobiose and D-Salicin, ATPase component (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC

Query= reanno::Smeli:SMc04256
         (361 letters)



>NCBI__GCF_000759345.1:WP_043527041.1
          Length = 354

 Score =  274 bits (701), Expect = 2e-78
 Identities = 156/345 (45%), Positives = 216/345 (62%), Gaps = 18/345 (5%)

Query: 1   MTSVSVRDLSLNF-GAVTVLDRLNLDIDHGEFLVLLGSSGCGKSTLLNCIAGLLDVSDGQ 59
           M S+ +  L   + G V  +  ++L+I  GEF+VL+G SGCGKSTLL  +AGL  ++DG 
Sbjct: 1   MASIQLTGLKKTYAGNVEAVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDGT 60

Query: 60  IFIKDRNVTWEEPKDRGIGMVFQSYALYPQMTVEKNLSFGLKVAKIPPAEIEKRVKRASE 119
           + I DR V   EP +R I MVFQ+YALYP MTV  NL++GLK   +   EIE+RV  A+ 
Sbjct: 61  LKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAAA 120

Query: 120 ILQIQPLLKRKPSELSGGQRQRVAIGRALVRDVDVFLFDEPLSNLDAKLRSELRVEIKRL 179
           +L+I+P L+RKP +LSGGQRQRVA+GRALVR+   FLFDEPLSNLDAKLR ++RVEIK+L
Sbjct: 121 MLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQL 180

Query: 180 HQSLKNTMIYVTHDQIEALTLADRIAVMKSGVIQQLADPMTIYNAPENLFVAGFIGSPSM 239
            + LK T +YVTHDQ+EALTL DR+ V+  G I+Q+  PM +Y  P ++FVA FIGSP+M
Sbjct: 181 QRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPAM 240

Query: 240 NFFRGEVEPKDGRSFVRAGGIAFDVTAYPAHTRLQPGQKVVLGLRPEHVKVDEARDGEPT 299
           N        + G     A G+   + A             V+G+RP+ ++++   +    
Sbjct: 241 NMLPVAYLRERG-----ANGLLDHLAA----------DTDVIGIRPDDLRIEAPDEDHLV 285

Query: 300 HQAVVDIEEPMGADNLLWLTFAGQSMSVRIAGQRRYP--PGSTVR 342
               V++ E  GA++ L+++  G      I    R P   G T+R
Sbjct: 286 VTGTVELFEAAGAESHLYVSLEGSDQPTVIRTSARPPVAEGETMR 330


Lambda     K      H
   0.320    0.137    0.392 

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: 339
Number of extensions: 8
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: 361
Length of database: 354
Length adjustment: 29
Effective length of query: 332
Effective length of database: 325
Effective search space:   107900
Effective search space used:   107900
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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