GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylT in Dyella japonica UNC79MFTsu3.2

Align Glucose/fructose transport protein (characterized, see rationale)
to candidate N515DRAFT_0382 N515DRAFT_0382 MFS transporter, sugar porter (SP) family

Query= uniprot:A0A0H3C6H3
         (478 letters)



>FitnessBrowser__Dyella79:N515DRAFT_0382
          Length = 472

 Score =  444 bits (1141), Expect = e-129
 Identities = 220/455 (48%), Positives = 308/455 (67%), Gaps = 4/455 (0%)

Query: 25  VAAIVAVATIGGFMFGYDSGVINGTQEGLESAFNLSKLGTGLNVGAILIGCAIGAFAAGR 84
           V  I A A +GGF+FG+D+ VING  + +  +F L     G  V   L+G A+GA+ AG 
Sbjct: 17  VVLIAAAAALGGFLFGFDTAVINGAVDAVRGSFGLGAGRIGFAVSCALLGSALGAWYAGP 76

Query: 85  LADVWGRRTVMIISALLFVISAIGTGAAESSIVFIIFRLIGGLGVGAASVLCPVYISEVT 144
           LAD WGR   M ++A+L  ISA+G+G        +++RL+GG+GVG ASV+ P YI+EV+
Sbjct: 77  LADRWGRVRTMQVAAVLLAISALGSGLVAGVWDLVLWRLVGGIGVGVASVIAPTYIAEVS 136

Query: 145 PANIRGRLSSVQQIMIITGLTGAFVANYALAHTAGSSTAEFWLGLPAWRWMFWMQIIPAG 204
           PA +RGRL S+QQ+ I+ G+  A +++  LA TAG ++ + WLGL AWRWMF + ++PA 
Sbjct: 137 PARVRGRLGSLQQLAIVLGIFAALLSDAWLAGTAGGASQKLWLGLEAWRWMFLVAVVPAL 196

Query: 205 VFFLCLLGIPESPRYLVAKGKDAQAEAILSRLFGAGQG---AKKVEEIRASLSADHKPTF 261
           ++   +LG+PESPR+LVAKG+  +A+ +L ++           K+ +I  SL ++++P  
Sbjct: 197 IYGSLVLGVPESPRHLVAKGRMDEAKQVLRQVLDLQDEHALQHKLGDIAQSLRSEYRPGL 256

Query: 262 SDLLDPTTKKLRVILWAGLVLAVFQQLVGINIVFYYGSVLWQSVGFTEDDSLKINILSGT 321
            DL       L V+ W G++L+VFQQ VGIN++FYY S LW SVGF+E D+  I++++  
Sbjct: 257 RDLRGSMAGLLPVV-WVGILLSVFQQFVGINVIFYYSSTLWHSVGFSESDAFSISVVTSV 315

Query: 322 LSILACLLAIGLIDKIGRKPLLLIGSAGMAVTLGVLTWCFSTATTVNGALTLGDQIGLTA 381
           +++L  L+AI L+D+IGRKPLL IGSAGM VTLG++ WCFS A     AL+L    G+ A
Sbjct: 316 VNVLVTLVAIALVDRIGRKPLLAIGSAGMTVTLGLMAWCFSQAAGSGAALSLPAPWGMVA 375

Query: 382 LIAANLYVIFFNLSWGPVMWVMLGEMFPNQMRGSALAVCGFAQWIANFAISVSFPALAAA 441
           L+AAN YV+FF LSWGP++WV+LGEMFPN++R  ALAV   AQW+ANF I+ SFPAL+  
Sbjct: 376 LVAANAYVVFFGLSWGPMVWVLLGEMFPNRIRAIALAVAAAAQWVANFIITSSFPALSEL 435

Query: 442 SLPMTYGFYALSAVVSFFLVQKLVHETRGKELEAM 476
            L   YG YA  A+VS   V K V ET+G ELE M
Sbjct: 436 GLSFAYGVYAFFALVSLVFVVKAVRETKGMELEEM 470


Lambda     K      H
   0.325    0.138    0.417 

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: 751
Number of extensions: 43
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: 478
Length of database: 472
Length adjustment: 33
Effective length of query: 445
Effective length of database: 439
Effective search space:   195355
Effective search space used:   195355
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 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