GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Slc2a5 in Pantoea rwandensis LMG 26275

Align sugar transport protein 13 (characterized)
to candidate WP_084936573.1 HA51_RS21365 sugar porter family MFS transporter

Query= CharProtDB::CH_091463
         (526 letters)



>NCBI__GCF_002095475.1:WP_084936573.1
          Length = 464

 Score =  214 bits (544), Expect = 7e-60
 Identities = 145/469 (30%), Positives = 238/469 (50%), Gaps = 41/469 (8%)

Query: 22  IVIISCIMAATGGLMFGYDVGVSGGVTSMPDFLEKFFPVVYRKVVAGADKDSNYCKYDNQ 81
           + +  C +AA  GL+FG D+GV  G  ++P F+ K F V   +                 
Sbjct: 15  MTLFVCFLAALAGLLFGLDIGVIAG--ALP-FIAKDFNVTAHQQ---------------- 55

Query: 82  GLQLFTSSLYLAGLTATFFASYTTRTLGRRLTMLIAGVFFIIGVALNAGAQDLAMLIAGR 141
             +   SS+          + + +  LGR+ +++   + F+IG   +A A    MLIA R
Sbjct: 56  --EWIVSSMMFGAAVGAVGSGWMSSRLGRKKSLMAGAILFVIGSLWSAMATSPDMLIAAR 113

Query: 142 ILLGCGVGFANQAVPLFLSEIAPTRIRGGLNILFQLNVTIGILFANLVNYGTAKIKGGWG 201
           ++LG  VG A+   PL+LSEIAP +IRG +  L+QL +TIGIL A L +  TA    G  
Sbjct: 114 VVLGLAVGVASYTAPLYLSEIAPEKIRGSMISLYQLMITIGILAAYLSD--TAFSDAG-A 170

Query: 202 WRLSLGLAGIPALLLTVGALLVTETPNSLVERGRLDEGKAVLRRIRGT-DNVEPEFADLL 260
           WR  LG+  IPA+LL +G   +  +P  L  +G     + VL R+R T +  + E  ++ 
Sbjct: 171 WRWMLGVITIPAILLLIGVFFLPNSPRWLAAKGDFRSAQRVLDRLRDTSEQAKRELDEIR 230

Query: 261 EASRLAKEVKHPFRNLLQRRNRPQLVIAVALQIFQQCTGINAIMFYAPVLFSTLGFGSDA 320
           E+ ++ +     F++      R  + + V LQ+ QQ TG+N IM+YAP +F   GF +  
Sbjct: 231 ESLKIKQSGWQLFQS--NSHFRRAVYLGVLLQVMQQFTGMNVIMYYAPKIFEIAGFANTT 288

Query: 321 -SLYSAVVTGAVNVLSTLVSIYSVDKVGRRVLLLEAGVQMFFSQVVIAIILGVKVTDTST 379
             ++  V+ G VNVL+T ++I  VD+ GR+  L+   + M     ++  +L + +   S 
Sbjct: 289 QQMWGTVIVGLVNVLATFIAIGLVDRWGRKPTLVLGFIVMAAGMGILGTMLHIGIHSASA 348

Query: 380 NLSKGFAILVVVMICTYVAAFAWSWGPLGWLIPSETFPLETRSAGQSVTVCVNLLFTFII 439
                     V M+  ++  FA S GPL W++ SE  PL+ R  G +V+   N +   I+
Sbjct: 349 Q------YFAVAMLLMFIVGFAMSAGPLIWVLCSEIQPLKGRDFGITVSTATNWIANMIV 402

Query: 440 AQAFLSMLCHF----KFGIFIFFSAWVLIMSVFVMFLLPETKNIPIEEM 484
              FL+ML        F ++   + + ++++V    L+PETKN+ +E +
Sbjct: 403 GATFLTMLNSLGNAPTFWVYAGLNVFFILLTV---ALIPETKNVSLEHI 448


Lambda     K      H
   0.326    0.141    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: 600
Number of extensions: 33
Number of successful extensions: 7
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: 526
Length of database: 464
Length adjustment: 34
Effective length of query: 492
Effective length of database: 430
Effective search space:   211560
Effective search space used:   211560
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: 52 (24.6 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