GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gluD in Nitratifractor salsuginis DSM 16511

Align GluD aka CGL1953, component of Glutamate porter (characterized)
to candidate WP_013554635.1 NITSA_RS08635 amino acid ABC transporter permease

Query= TCDB::P48245
         (273 letters)



>NCBI__GCF_000186245.1:WP_013554635.1
          Length = 384

 Score = 81.3 bits (199), Expect = 3e-20
 Identities = 46/116 (39%), Positives = 74/116 (63%), Gaps = 1/116 (0%)

Query: 102 FAAVVFGLTMYNGSVIAEILRSGIASLPKGQKEAAIALGMSSRQTTWSILLPQAVAAMLP 161
           F A++F L++Y  + IAE +RSGI ++PKGQKEAA +LG+S  Q    ++LPQAV   +P
Sbjct: 252 FLALLFALSIYTATFIAEAIRSGIEAVPKGQKEAATSLGLSPLQQLRLVILPQAVRIAIP 311

Query: 162 ALISQMVIALKDSALGYQIGYIEVVRSGIQSASVNRNYLAALFVVALIMIVLNFSL 217
           ++I+Q +  +K+S+L   IGY E+V +     S+N+   A   ++  ++  L  SL
Sbjct: 312 SIINQYLNLIKNSSLAAAIGYPELV-TIFAGTSLNQTGQALEILLITMLTYLLISL 366



 Score = 43.9 bits (102), Expect = 5e-09
 Identities = 23/74 (31%), Positives = 40/74 (54%)

Query: 15  PFINSQTWTTYILPGLWGTLKSAVFSVILALVMGTALGLGRISEIRILRWFCAVIIETFR 74
           PF  + T       GL  TL  + + ++ + ++G  +G+ R+S   ++    A  IETFR
Sbjct: 64  PFTPASTHLKVFEVGLLNTLIVSFWGIVFSSLIGLLIGIWRLSPNWLINRIAAAYIETFR 123

Query: 75  AIPVLILMIFAYQM 88
            IPVL+ ++F Y +
Sbjct: 124 NIPVLLQILFWYNV 137


Lambda     K      H
   0.323    0.136    0.395 

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: 226
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 273
Length of database: 384
Length adjustment: 28
Effective length of query: 245
Effective length of database: 356
Effective search space:    87220
Effective search space used:    87220
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Apr 09 2024. 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