GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltS in Shewanella sp. ANA-3

Align Sodium/glutamate symporter; Glutamate permease (characterized)
to candidate 7024349 Shewana3_1541 sodium/glutamate symporter (RefSeq)

Query= SwissProt::P0AER8
         (401 letters)



>FitnessBrowser__ANA3:7024349
          Length = 407

 Score =  351 bits (901), Expect = e-101
 Identities = 192/410 (46%), Positives = 269/410 (65%), Gaps = 28/410 (6%)

Query: 2   FHLDTLATLVAATLTLLLGRKLVHSVSFLKKYTIPEPVAGGLLVALALLVLKKSMGWEVN 61
           + +  L + + A   L +G  +   V   ++Y IPEP+ GGL+VA A++         + 
Sbjct: 5   YTIGELESFLIAIFVLFIGHSINRHVRVFRQYNIPEPIVGGLVVA-AVVAFLHFQDITLA 63

Query: 62  FDMSLRDPLMLAFFATIGLNANIASLRAGGRVVGIFLIVVVGLLVMQNAIGIGMASLLGL 121
           F + +++ LML FF+TIGL+AN   L +GG+ V IFL V    +V+QNA+G+ +ASLLGL
Sbjct: 64  FSLPMQNTLMLMFFSTIGLSANYKLLLSGGKKVFIFLGVASVYIVIQNAVGVSLASLLGL 123

Query: 122 DPLMGLLAGSITLSGGHGTGAAWSKLFIERYGFTNATEVAMACATFGLVLGGLIGGPVAR 181
           DP++GL+AGSITLSGGHGTG AWS+ F E YG  N  E+AMA ATFGLV+GG+IGGPVA+
Sbjct: 124 DPILGLIAGSITLSGGHGTGVAWSQTFAENYGI-NTLELAMAAATFGLVMGGIIGGPVAQ 182

Query: 182 YLV--------------KHSTTPNGIPDDQEVPTAFEKPDVGRMITSLVLIETIALIAIC 227
            L+               H+T P  +  DQ      E+  V    T+  +IET+ ++ IC
Sbjct: 183 RLIGKHNLVSSYGMGRKHHATHPQLVTYDQ-----LEEDQV----TAKTIIETLFVLLIC 233

Query: 228 LTVGKIVAQLLAGTAF---ELPTFVCVLFVGVILSNGLSIMGFYRVFERAVSVLGNVSLS 284
           +   K    L++       ++P FV  LF+GVI++N   +   Y+    ++ V+G V+LS
Sbjct: 234 VAGAKWFTVLVSEYQLNWLKMPDFVYALFLGVIIANITEVTRGYKPHTESIDVIGTVALS 293

Query: 285 LFLAMALMGLKLWELASLALPMLAILVVQTIFMALYAIFVTWRMMGKNYDAAVLAAGHCG 344
           LFL+MALM LKLWE+  LA+P+L IL+VQT  +A++A FVT+++MG NYDAAV+  GHCG
Sbjct: 294 LFLSMALMNLKLWEILDLAIPLLIILLVQTAVLAVFAYFVTFKIMGSNYDAAVITGGHCG 353

Query: 345 FGLGATPTAIANMQAITERFGPSHMAFLVVPMVGAFFIDIVNALVIKLYL 394
           FG+GATPTA+ NM A+  R GPS  AF+VVP+VGAFFIDIVN +V++ YL
Sbjct: 354 FGMGATPTAVMNMGALVSRTGPSPQAFMVVPIVGAFFIDIVNLIVLQGYL 403


Lambda     K      H
   0.329    0.143    0.421 

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: 399
Number of extensions: 14
Number of successful extensions: 5
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: 401
Length of database: 407
Length adjustment: 31
Effective length of query: 370
Effective length of database: 376
Effective search space:   139120
Effective search space used:   139120
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 (21.8 bits)
S2: 50 (23.9 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