GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltJ in Nitratifractor salsuginis DSM 16511

Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate WP_013554635.1 NITSA_RS08635 amino acid ABC transporter permease

Query= reanno::pseudo1_N1B4:Pf1N1B4_772
         (248 letters)



>NCBI__GCF_000186245.1:WP_013554635.1
          Length = 384

 Score = 80.1 bits (196), Expect = 6e-20
 Identities = 43/133 (32%), Positives = 77/133 (57%), Gaps = 1/133 (0%)

Query: 108 TSAFLSVVVCLGLFTTARVCEQVRTGIQALPRGQEAAARAMGFKLPQIYWNVLLPQAYRI 167
           T  FL+++  L ++T   + E +R+GI+A+P+GQ+ AA ++G    Q    V+LPQA RI
Sbjct: 249 TPEFLALLFALSIYTATFIAEAIRSGIEAVPKGQKEAATSLGLSPLQQLRLVILPQAVRI 308

Query: 168 IIPPLTSEFLNVFKNSSVASLIGLMELLAQTKQTA-EFSANLFEAFTLATLIYFTLNMSL 226
            IP + +++LN+ KNSS+A+ IG  EL+     T+   +    E   +  L Y  +++ +
Sbjct: 309 AIPSIINQYLNLIKNSSLAAAIGYPELVTIFAGTSLNQTGQALEILLITMLTYLLISLIV 368

Query: 227 MLLMRSVEKKVAV 239
            L++     K+ +
Sbjct: 369 SLILNWFNAKMKI 381



 Score = 55.8 bits (133), Expect = 1e-12
 Identities = 24/67 (35%), Positives = 43/67 (64%)

Query: 28  GLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFRNVPLLVQLFIWYFL 87
           GL  T+ ++    + + L+G ++G+ R  PN +++ IA  Y+E FRN+P+L+Q+  WY +
Sbjct: 78  GLLNTLIVSFWGIVFSSLIGLLIGIWRLSPNWLINRIAAAYIETFRNIPVLLQILFWYNV 137

Query: 88  VPDLLPA 94
           V   LP+
Sbjct: 138 VLATLPS 144


Lambda     K      H
   0.326    0.140    0.433 

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: 219
Number of extensions: 10
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: 248
Length of database: 384
Length adjustment: 27
Effective length of query: 221
Effective length of database: 357
Effective search space:    78897
Effective search space used:    78897
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: 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