GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12060 in Collimonas pratensis Ter91

Align ABC transporter permease; SubName: Full=Monosaccharide ABC transporter membrane protein, CUT2 family; SubName: Full=Sugar ABC transporter permease (characterized, see rationale)
to candidate WP_061945961.1 CPter91_RS07485 ribose ABC transporter permease

Query= uniprot:A0A1N7UKA9
         (325 letters)



>NCBI__GCF_001584185.1:WP_061945961.1
          Length = 328

 Score =  253 bits (646), Expect = 5e-72
 Identities = 150/327 (45%), Positives = 207/327 (63%), Gaps = 9/327 (2%)

Query: 1   MNAKTITAPVTAAPRNRLRLSLDRFGLPLVFILLCVVMAFSSEYFMTWRNWMDILRQTSI 60
           M A +     T   R +LR  L   G+  V +LL +  A  SE F T +N   I +Q S+
Sbjct: 1   MEASSRITAETIGKREQLRGLLRTVGMLPVLLLLVLGFALMSENFFTVQNLSIITQQASV 60

Query: 61  NGILAVGMTYVILTKGIDLSVGSILAFAGLCSAMVATQGYGLLAAVSAGMFAGAMLGVVN 120
           N +LA GMT+VILT GIDLSVG+ILA A + + + +      +  ++AG+  G +LG+ N
Sbjct: 61  NIVLAAGMTFVILTAGIDLSVGAILAAAAVVAMLASLSPQFGMLGIAAGIGFGLLLGLAN 120

Query: 121 GFMVANLSIPPFVATLGMLSIARGMTFILNDGSPI--TDLPDAYLALGIGKIGPIGVP-- 176
           G ++A + +PPF+ TLG L+  RG+  +L D   +   DLP A+    IG    +GVP  
Sbjct: 121 GALIAFMRLPPFIVTLGALTAMRGLARLLADDKTVFNPDLPFAF----IGNDSLLGVPWL 176

Query: 177 IIIFAVVALIFWMVLRYTTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAG 236
           +II  VV  + W +LR T  G  +YAVGGN ++AR SGI V KV+  VY VSGLLAGL  
Sbjct: 177 VIIALVVVALSWFILRRTVIGVQIYAVGGNHEAARLSGIKVWKVLLFVYAVSGLLAGLGA 236

Query: 237 VVLSARTTSALP-QAGVSYELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNL 295
           V+ ++R ++A   Q G SYELDAIAAV++GGTS +GG GSI GTL GAL+I V+ NGL L
Sbjct: 237 VMTASRLSAANGLQLGQSYELDAIAAVILGGTSFTGGVGSIGGTLIGALIIAVLTNGLVL 296

Query: 296 LGVSSYYQQVAKGLIIVFAVLIDVWRK 322
           LGVS  +Q + KG++I+ AV +D +R+
Sbjct: 297 LGVSDIWQYIIKGIVIIGAVALDRYRQ 323


Lambda     K      H
   0.326    0.141    0.412 

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: 296
Number of extensions: 16
Number of successful extensions: 3
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: 325
Length of database: 328
Length adjustment: 28
Effective length of query: 297
Effective length of database: 300
Effective search space:    89100
Effective search space used:    89100
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 (21.6 bits)
S2: 48 (23.1 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