Align ABC transporter permease (characterized, see rationale)
to candidate WP_052665280.1 NITAL_RS06395 sugar ABC transporter permease
Query= uniprot:A0A165KPZ4 (293 letters) >NCBI__GCF_000969705.1:WP_052665280.1 Length = 313 Score = 130 bits (328), Expect = 3e-35 Identities = 83/273 (30%), Positives = 144/273 (52%), Gaps = 10/273 (3%) Query: 13 LVVAPAFVLGFAFIYGLMVWNGVLSLTVSRMLPNYEWAGLAQYERLWEMDRWWVALKNLG 72 L++APA++ AF+ G ++ L+LT +L + E+ GL + R+ R V +N Sbjct: 33 LMIAPAYLFFVAFVLGPLLTVFWLALTRYNLLTSPEFVGLDNFARMGSDGRLHVVFRNTL 92 Query: 73 IFGVGYVGGSLLIGVVLAVLLDQKI--RAEGALRTIYLYPMALSFVVTGTAWKWLLNPGL 130 I+ V V G++LAVLL++++ R ALR+ Y +P ++ V W++LL + Sbjct: 93 IYVVAAVVLMNAFGLLLAVLLNRRMNPRVRTALRSAYFFPSLVALVYVSIIWQFLLQYDV 152 Query: 131 GI-EKMVRDWGFPNFEFGWLVDTEMAIYCVVIAGIWQSAGFAMALFLAGLRGIDDSIIKA 189 G+ + + G P WL + + V+ +W++ GFAM ++LA L+ + ++A Sbjct: 153 GVVNHYLTEGGGPRLN--WLGGYPLGLVSVIAVDVWRNTGFAMLIYLAALQDVPSERLEA 210 Query: 190 AQVDGASLPRIYWRIVLPALRPVFFSTLMVLSHLAIKSFDLVMALTAGGPGFATDVPATF 249 A VDGA+ R +W + LP + P + + + A + F+ ++ LT GGPG AT + Sbjct: 211 AAVDGAAGWRRFWHVSLPVISPAVLFNVFLTNIGAWQIFESIVVLTGGGPGDATRSITMY 270 Query: 250 MYTMSFSRGQIGLGAA-----SATMMLATVAAL 277 +Y +F ++G +A A M+LAT A L Sbjct: 271 LYERAFQSFEMGYASAIAVVLFAVMLLATAALL 303 Lambda K H 0.327 0.141 0.451 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: 282 Number of extensions: 20 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: 293 Length of database: 313 Length adjustment: 27 Effective length of query: 266 Effective length of database: 286 Effective search space: 76076 Effective search space used: 76076 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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:
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