Align ABC transporter permease (characterized, see rationale)
to candidate WP_049992209.1 LT39_RS19805 sugar ABC transporter permease
Query= uniprot:A0A165KPZ4 (293 letters) >NCBI__GCF_000784335.1:WP_049992209.1 Length = 317 Score = 151 bits (382), Expect = 2e-41 Identities = 97/270 (35%), Positives = 146/270 (54%), Gaps = 7/270 (2%) Query: 17 PAFVLGFAFIYGLMVWNGVLSLTVSRML--PNYEWAGLAQYERLWEMDRWWVALKNLGIF 74 P ++G A +YG + +N +S T + P + L Y + + A N + Sbjct: 42 PFILMGIA-VYGGIGYNIAISFTDYAGIGQPTFSSFDLEMYREALASEAFREAAFNNFVL 100 Query: 75 GVGYVGGSLLIGVVLAVLLDQKIRAEGALRTIYLYPMALSFVVTGTAWKWLLNPGLGI-E 133 + + SL +G+ LA+LLD IR + ++TIYL PMALSFVVT W W+ NP G+ Sbjct: 101 LIAFTTISLALGLFLAILLDHGIRYKDKIQTIYLLPMALSFVVTAQLWLWMFNPESGVLT 160 Query: 134 KMVRDWGFPNFEFGWLVDTEMAIYCVVIAGIWQSAGFAMALFLAGLRGIDDSIIKAAQVD 193 +V GF + WL + +A+ V+ A +WQ +G+AM ++LAGL+ I +AA VD Sbjct: 161 VIVTTLGFEPID--WLGNPRLALPAVIFALVWQFSGYAMVVYLAGLQSIPADQFEAANVD 218 Query: 194 GASLPRIYWRIVLPALRPVFFSTLMVLSHLAIKSFDLVMALTAG-GPGFATDVPATFMYT 252 GAS R Y RI++P L+ S +VL A+K+F + +L P TD+ AT M Sbjct: 219 GASTIRTYLRIIVPQLKESSVSAAVVLMVFALKAFTFLYSLVGQYRPPNGTDILATLMVR 278 Query: 253 MSFSRGQIGLGAASATMMLATVAALVIPYL 282 +F G+ GAA ATM+L +++ PYL Sbjct: 279 QAFKFGKWAYGAAIATMLLLLALSVIAPYL 308 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: 268 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: 293 Length of database: 317 Length adjustment: 27 Effective length of query: 266 Effective length of database: 290 Effective search space: 77140 Effective search space used: 77140 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