GapMind for catabolism of small carbon sources

 

Alignments for a candidate for galP in Williamsia sterculiae CPCC 203464

Align Arabinose-proton symporter; Arabinose transporter (characterized)
to candidate WP_076479258.1 BW971_RS10475 sugar porter family MFS transporter

Query= SwissProt::P96710
         (464 letters)



>NCBI__GCF_900156495.1:WP_076479258.1
          Length = 495

 Score =  291 bits (745), Expect = 3e-83
 Identities = 163/459 (35%), Positives = 264/459 (57%), Gaps = 23/459 (5%)

Query: 23  VILISCAAGLGGLLYGYDTAVISGAIGFLKDLYSLSPFMEGLVISSIMIGGVVGVGISGF 82
           V+ I+  A LGGLL+GYD+AVI+GA+  ++D + ++    G  ++S ++G   G   +G 
Sbjct: 25  VVRIASVAALGGLLFGYDSAVINGAVSSIQDDFHVADSTLGFAVASALLGAAAGAFSAGR 84

Query: 83  LSDRFGRRKILMTAALLFAISAIVSALSQDVSTLIIARIIGGLGIGMGSSLSVTYITEAA 142
           L+DR GR K++   A+LF ISAI +A + ++ TL++ R++GG+G+G+ S ++  YI E +
Sbjct: 85  LADRIGRLKVMKIGAVLFFISAIGTAFAPEIWTLVLFRVVGGIGVGVASVIAPAYIAETS 144

Query: 143 PPAIRGSLSSLYQLFTILGISATYFIN-LAVQRSGTYEWGVHTG---WRWMLAYGMVPSV 198
           PP +RG L SL QL  +LGI  +  ++ L    +G     +  G   WRWM     +P+V
Sbjct: 145 PPRVRGRLGSLQQLAIVLGIFLSLLVDYLLAHIAGGANEKLALGLDAWRWMFLAMAIPAV 204

Query: 199 IFFLVLLVVPESPRWLAKAGKTNEALKILTRINGETVAKEELKNIENSLKIEQMGSLSQL 258
           ++ L+   +PESPR+L    +  EA ++LT + GE   +  +  I++SL  +   S   L
Sbjct: 205 VYGLLASTIPESPRYLVATQRLPEARRVLTLLFGEKNLELTITRIQDSLAGDTKPSWKDL 264

Query: 259 FKP---GLRKALVIGILLALFNQVIGMNAITYYGPEIFKMMGFGQNAGFVTTCIVGVVEV 315
            +P   G+   + +G+LL++F Q +G+N I YY   +++ +GF +N  F T+    +V +
Sbjct: 265 ARPGGGGIYPIVWVGLLLSVFQQAVGINVIFYYSNILWEAVGFKENQAFQTSVFTSLVNI 324

Query: 316 IFTVIAVLLIDKVGRKKLMSIGSAFMAIFM----ILIGTSFYFELTSGIM---------M 362
           + T +A+ L+DK+GRK L+ IGSA MA+ +    I  GT+       G+M          
Sbjct: 325 VATFVAIALVDKIGRKPLLLIGSAGMAVTLGVMAICFGTAAQQPNADGVMEPHLTGAAGP 384

Query: 363 IVLILG--FVAAFCVSVGPITWIMISEIFPNHLRARAAGIATIFLWGANWAIGQFVPMMI 420
           I LI    FV  F +S GP+ W+++ EIFPN +R  A  +A    W ANWAI    P  +
Sbjct: 385 IALIAANLFVVFFALSWGPVVWVLLGEIFPNRIRGAALSLAAAGQWAANWAITVSFP-SL 443

Query: 421 DSFGLAYTFWIFAVINILCFLFVVTICPETKNKSLEEIE 459
            SF L + + ++A+  +L  LFV     ETK  SLE+++
Sbjct: 444 KSFSLGFAYGMYALFAVLSLLFVARFVRETKGMSLEDMD 482


Lambda     K      H
   0.327    0.142    0.425 

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: 507
Number of extensions: 27
Number of successful extensions: 6
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: 464
Length of database: 495
Length adjustment: 34
Effective length of query: 430
Effective length of database: 461
Effective search space:   198230
Effective search space used:   198230
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 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