GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_12060 in Alkalihalobacterium alkalinitrilicum DSM 22532

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_078430749.1 BK574_RS01735 ABC transporter permease

Query= uniprot:A0A1N7UKA9
         (325 letters)



>NCBI__GCF_002019605.1:WP_078430749.1
          Length = 321

 Score =  186 bits (471), Expect = 9e-52
 Identities = 97/285 (34%), Positives = 167/285 (58%), Gaps = 1/285 (0%)

Query: 33  LLCVVMAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGSILAFAGLCS 92
           ++ +    S   F ++ N+++I RQ S   I+A+G T V+  K  DLS+G++ +  G+ S
Sbjct: 28  IIIIFSILSPSSFASFDNFINITRQISFLVIIALGATLVMAVKEFDLSIGAMASLGGVLS 87

Query: 93  AMVATQGYGLLAAVSAGMFAGAMLGVVNGFMVANLSIPPFVATLGMLSIARGMTFILNDG 152
           A++A  G  ++  +   +  G ++G  NG +V    +  FV TL M ++  G+TF L  G
Sbjct: 88  ALLAASGTPIIFCLLVPIIVGFVVGFFNGAIVTKFKVLSFVTTLAMGTVIGGVTFWLTGG 147

Query: 153 SPITD-LPDAYLALGIGKIGPIGVPIIIFAVVALIFWMVLRYTTYGRYVYAVGGNEKSAR 211
           + + + +P+ +  LG  K+  +    +I  V+ +IFW ++  T+ GR +YA+GGNEK++ 
Sbjct: 148 ATVFENIPEGFKFLGQSKLAFLPTLSVIMFVLVIIFWYIMSQTSLGRRLYAIGGNEKASE 207

Query: 212 TSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVSYELDAIAAVVIGGTSLSG 271
            SGI + +     + + G+LA   G +L++R  SA P  G  + L+A AAV +G T +  
Sbjct: 208 VSGINIARYKNIAFALCGMLAAFTGALLASRLGSAHPTGGDGFFLNAYAAVFLGMTIVKN 267

Query: 272 GTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVFAVL 316
           G  +I+GTLFGA +IG++ NGL +L V S+ Q +  G II+ A++
Sbjct: 268 GVPNILGTLFGAAIIGIMANGLTILEVPSFIQNIITGAIIIIALI 312


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: 221
Number of extensions: 16
Number of successful extensions: 2
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: 321
Length adjustment: 28
Effective length of query: 297
Effective length of database: 293
Effective search space:    87021
Effective search space used:    87021
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 Apr 09 2024. 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