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_040660796.1 ON16_RS07490 sodium:glutamate symporter

Query= SwissProt::P0AER8
         (401 letters)



>NCBI__GCF_000307265.1:WP_040660796.1
          Length = 416

 Score =  208 bits (530), Expect = 2e-58
 Identities = 127/396 (32%), Positives = 214/396 (54%), Gaps = 11/396 (2%)

Query: 2   FHLDTLATLVAATLTLLLGRKLVHSVSFLKKYTIPEPVAGGLLVALALLVLKKSMGWEVN 61
           F  + L+ L  A   + LGR +V     L+KY IP PV  GL+ +L +  +K S     +
Sbjct: 22  FKFEYLSALGFAAFVIFLGRAIVRHSKLLQKYAIPAPVVSGLIFSLVVSFIKMSGAMAFS 81

Query: 62  FDMS-LRDPLMLAFFATIGLNANIASLR-AGGRVVGIFLIVVVGLLVMQNAIGIGMASLL 119
           FD++ ++D     FF  +G   +   ++ AGG++  +  +    L+ +Q+ +G+ + +L+
Sbjct: 82  FDVTVMKDLCQNLFFLCVGFGFSWKMIKHAGGKLCVLIAVGACLLITLQDLLGVAIGNLV 141

Query: 120 GLDPLMGLLAGSITLSGGHGTGAAWSKLFIERYGFTNATEVAMACATFGLVLGGLIGGPV 179
           GL PL+ L   S  +SGG GT +A+  +F E  G   AT + +A  T G ++G LIGGPV
Sbjct: 142 GLHPLLALQCSSSAMSGGVGTASAFGPIF-ENMGAPEATTIGVAAGTLGNIMGSLIGGPV 200

Query: 180 ARYLVKHSTTPNGIPDDQEVPTAFE--KPDVGRMITSLVLIETIALIAICLTVGKIVAQL 237
           A +L+          D  E   + E  + D GRMI+   +   +A + +      I   L
Sbjct: 201 AAFLISRHGLKADPNDKPEAVMSGEATRLDNGRMISMFAMCLLLAALGM-----PIYMLL 255

Query: 238 LAGTAFELPTFVCVLFVGVILSNGLSIMGFYRVFERAVSVLGNVSLSLFLAMALMGLKLW 297
            +    E+P F+  LF G I  N +      + +   V  + ++ L L+LA+ LM + + 
Sbjct: 256 DSIPMIEMPKFIGCLFAGAIARNVMEAFHI-KFYTPEVDAIEHMFLELYLALVLMTIDIT 314

Query: 298 ELASLALPMLAILVVQTIFMALYAIFVTWRMMGKNYDAAVLAAGHCGFGLGATPTAIANM 357
           +LA +A  M  IL+ Q I MAL+ IFV++ M G++Y AAV+AAG+CG+G G+ P A+AN 
Sbjct: 315 KLAPVAGQMGVILIGQAILMALFGIFVSYNMFGRDYGAAVMAAGNCGWGCGSGPNAVANE 374

Query: 358 QAITERFGPSHMAFLVVPMVGAFFIDIVNALVIKLY 393
           +A+ +++G  ++A+++ P       DI N + + L+
Sbjct: 375 KAVMDQYGWHNIAWVLYPSFAVIIDDIYNPIFLSLF 410


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: 381
Number of extensions: 12
Number of successful extensions: 4
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: 416
Length adjustment: 31
Effective length of query: 370
Effective length of database: 385
Effective search space:   142450
Effective search space used:   142450
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