GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SSS-glucose in Echinicola vietnamensis KMM 6221, DSM 17526

Align Renal Na+:D-glucose symporter type 1 (Sglt1; Slc5a1) of 662 aas and 14 TMSs (characterized)
to candidate Echvi_1680 Echvi_1680 transporter, SSS family

Query= TCDB::Q2A687
         (662 letters)



>FitnessBrowser__Cola:Echvi_1680
          Length = 528

 Score =  278 bits (710), Expect = 6e-79
 Identities = 163/536 (30%), Positives = 281/536 (52%), Gaps = 51/536 (9%)

Query: 27  PADISVIVIYFLLVLAVGIWAMVQSNRGTVGGFFLAGRSMSWWPIGASLFASNIGSGHFV 86
           P D +V+ +Y + ++ +G W   +  R      FLAG S+ W  IG +++ +N+G    +
Sbjct: 9   PLDFAVLGLYLVTLIGIGYWVSFKKKRDADENLFLAGNSLGWPSIGFTMWGTNVGPSMLI 68

Query: 87  GLAGNGAAGGLATGGFEWNALVIVIVLGWLFVPIYIRAGVVTMPEYLKKRFGGNRIRIYL 146
             A  G   G+  G F W A + + +L  +F P Y+ A V T+PE++ KRFG +   I L
Sbjct: 69  ASASIGYTTGVVAGNFAWYAFIFIFLLAVVFAPRYLGARVQTLPEFMGKRFGSSTQNI-L 127

Query: 147 SVLSLFLYIFTKISADMFSGAIFIREALGLNIYVAVVILLSITALYTVTGGLAAVIYTDT 206
           +  ++   + + +S  +F+G I IR+ L L ++++VVIL+ I A +T+ GGL A+ YT+ 
Sbjct: 128 AWYTIVTVLISWLSLTLFAGGILIRQILDLPLWLSVVILILIAAFFTIAGGLKAIAYTNV 187

Query: 207 LQTIIMVVGSFILMGYAFNAVGGYEAMREKYMNAITTQTFDPVLNISANCYTPRSDSFHL 266
            Q ++++V S  L       VGG                   V  + AN  TP  + ++L
Sbjct: 188 FQMVLLIVVSLALTLTGLYKVGG-------------------VGELIAN--TP-GEYWNL 225

Query: 267 FRNPLTADLPWPGLIFGLSILAIWYWCTDQVIVQRCLSAKNMSHVKAGCVLCGYLKLLPM 326
                  + PW  +  G  ++ +W+WCTDQ +VQ  L AKN+   + G    G+LK+L +
Sbjct: 226 LLPADDPNYPWVAIALGYPVMGVWFWCTDQSMVQSVLGAKNLKEGQLGANFTGWLKILDV 285

Query: 327 YLMVFPGMISRILYTDTIACVVPSLCKQYCDTEVGCSNIAYPTLVVRLMPAGLRGLMLSV 386
            L + PG+I  +L+ D                 +   + AY T+V +L P G+ GL+++V
Sbjct: 286 ALFIIPGIICYVLFPD-----------------LDNPDEAYMTMVTKLFPVGMTGLVMAV 328

Query: 387 MLASLMSSLTSIFNSASTLFTMDIWT-KIRPKATEKELMLAGRVFTLVLIAISIAWIPIV 445
           ++A+L+S++ S  N+ ST+FTMDI+  K +P+AT+K+++  GRV T++   I+I     +
Sbjct: 329 LIAALVSTIDSALNALSTVFTMDIYVKKYKPEATQKQIVTIGRVVTVLGAVIAIFLTLAI 388

Query: 446 QTAQSGKLFDYIQSVTSYLGPPIASVFLLGIFVKRTNEKGAFWGLIFGLAMGLS-RMIPE 504
            + +   LFD  QS+  ++ PP++ VFL G+  K+T  K A   L+FG  + L   ++  
Sbjct: 389 DSIKGLNLFDVFQSILGFIAPPMSVVFLFGVLWKKTTTKAANTVLLFGTILSLGIGVLYL 448

Query: 505 FVFGTGSCVRPSNCPLIICGIHYLYFAIILFVATCLLVLIISLLTKPIEDKHLHRL 560
           +VF                  H+L  +  +FV    L+++IS + +  +D H+  L
Sbjct: 449 WVFPNAE---------YAFWPHFLLLSFYIFVFLAALIVVISYVERNRKDLHVSTL 495


Lambda     K      H
   0.326    0.141    0.442 

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: 926
Number of extensions: 41
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: 662
Length of database: 528
Length adjustment: 37
Effective length of query: 625
Effective length of database: 491
Effective search space:   306875
Effective search space used:   306875
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: 53 (25.0 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