GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artQ in Lutibaculum baratangense AMV1

Align ABC transporter for L-Arginine, permease component 1 (characterized)
to candidate WP_023431720.1 N177_RS07670 ABC transporter permease subunit

Query= reanno::WCS417:GFF4244
         (229 letters)



>NCBI__GCF_000496075.1:WP_023431720.1
          Length = 234

 Score =  197 bits (502), Expect = 1e-55
 Identities = 102/224 (45%), Positives = 147/224 (65%)

Query: 4   GYGAVILDGAWLTLQLALSSMALAIVLGLIGVALRLSPVRWLAWLGDLYSTVIRGIPDLV 63
           G+G  +L GA LTLQ+AL S A+ + LGL+G A +LS    LA  G++Y+T++R +P+L+
Sbjct: 11  GWGGALLRGALLTLQIALLSYAIGLALGLLGAAAKLSGSPVLAGAGEVYTTLVRAVPELL 70

Query: 64  LILLIFYGGQDLLNRVAPMLGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKG 123
           LI+L+FYGG  +L      LG+   + ++  AA I  LG + GAY +E  RGA  AIP G
Sbjct: 71  LIILLFYGGSTMLEMALIALGFPGAVQVSGFAAAIAVLGVVQGAYQTEVIRGAIEAIPVG 130

Query: 124 QAEAGLAYGMSSFQVFFRVMVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQ 183
           Q EA  A+GMS      R+++P ++ +A+PGF N WL+L K TALIS+VG+ ++++  KQ
Sbjct: 131 QIEAARAFGMSPSLRLRRIVIPALLPIALPGFANLWLILLKDTALISIVGISELLYVGKQ 190

Query: 184 AADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVGVRAA 227
           AA ATR  F F+  V A+YL +T VS  A R +E+R   G+ AA
Sbjct: 191 AAGATRHYFFFYCVVGAIYLAMTLVSNGAFRLIERRVRRGIPAA 234


Lambda     K      H
   0.329    0.143    0.424 

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: 183
Number of extensions: 10
Number of successful extensions: 1
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: 229
Length of database: 234
Length adjustment: 23
Effective length of query: 206
Effective length of database: 211
Effective search space:    43466
Effective search space used:    43466
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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