GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltS in Oscillibacter ruminantium GH1

Align Sodium/glutamate symporter; Glutamate permease (characterized)
to candidate WP_040663080.1 ON16_RS12165 sodium/glutamate symporter

Query= SwissProt::P0AER8
         (401 letters)



>NCBI__GCF_000307265.1:WP_040663080.1
          Length = 389

 Score =  304 bits (778), Expect = 3e-87
 Identities = 162/389 (41%), Positives = 239/389 (61%), Gaps = 5/389 (1%)

Query: 9   TLVAATLTLLLGRKLVHSVSFLKKYTIPEPVAGGLLVALALLVLKKSMGWEVNFDMSLRD 68
           TL  A + L +G  L   ++FL+K+ IP PV GGLL A+A  +L      E  FD +L++
Sbjct: 4   TLCVAVIVLFIGSALKKRINFLEKFCIPAPVVGGLLFAIATCILYALGIMEFTFDETLKN 63

Query: 69  PLMLAFFATIGLNANIASLRAGGRVVGIFLIVVVGLLVMQNAIGIGMASLLGLDPLMGLL 128
             M+ FF ++G  AN+  L++GG  + + L  VV L++ QN + +G+ASLL LDP++GL 
Sbjct: 64  VCMVLFFTSVGFQANLKVLKSGGIQLIVLLACVVVLMIAQNGLAVGLASLLNLDPMIGLC 123

Query: 129 AGSITLSGGHGTGAAWSKLFIERYGFTNATEVAMACATFGLVLGGLIGGPVARYLV-KHS 187
            GSI + GGH T  A+ K+ ++  G   A  +A A ATFGLV G L+GGP+ R L+ KH 
Sbjct: 124 TGSIPMVGGHATAGAFGKV-LQDLGVDGAVTLATAAATFGLVAGSLLGGPLGRRLIMKHD 182

Query: 188 TTPNGIPDDQEVPTAFEKPDVGRMITSLVLIETIALIAICLTVGKIVAQLLAGTAFELPT 247
                +  D  V    E+  + ++    +    +  + + + +G IV+ LL  T    P 
Sbjct: 183 LLKTAVKADDSVLVEDEEKHLRKVS---MYQPAVYQLVLAMGIGTIVSALLTKTGLTFPI 239

Query: 248 FVCVLFVGVILSNGLSIMGFYRVFERAVSVLGNVSLSLFLAMALMGLKLWELASLALPML 307
           ++  + V  ++ N     G Y V    +  LGN++LSLFL +A++ LKLW+LA LALP++
Sbjct: 240 YIGAMIVAAVIRNVGEFTGKYTVHMGEIEDLGNIALSLFLGIAMITLKLWQLAELALPLV 299

Query: 308 AILVVQTIFMALYAIFVTWRMMGKNYDAAVLAAGHCGFGLGATPTAIANMQAITERFGPS 367
            +L  Q + MAL+A FV + +MG++YDAAVL AG CGFG+GATP A+ANMQAIT+R+ PS
Sbjct: 300 VLLTGQFLLMALFAYFVVYNVMGRDYDAAVLTAGTCGFGMGATPNAMANMQAITQRYAPS 359

Query: 368 HMAFLVVPMVGAFFIDIVNALVIKLYLML 396
             AFL+VP+VG+ F D  N LVI  ++ L
Sbjct: 360 VKAFLLVPLVGSLFADFFNTLVITFFINL 388


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: 346
Number of extensions: 11
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: 401
Length of database: 389
Length adjustment: 31
Effective length of query: 370
Effective length of database: 358
Effective search space:   132460
Effective search space used:   132460
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 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