Align Sugar transport system permease protein aka TT_C0326, component of The glucose/mannose porter TTC0326-8 plus MalK1 (ABC protein, shared with 3.A.1.1.25) (characterized)
to candidate H281DRAFT_03232 H281DRAFT_03232 carbohydrate ABC transporter membrane protein 2, CUT1 family
Query= TCDB::Q72KX4 (268 letters) >FitnessBrowser__Burk376:H281DRAFT_03232 Length = 283 Score = 171 bits (434), Expect = 1e-47 Identities = 91/256 (35%), Positives = 153/256 (59%), Gaps = 4/256 (1%) Query: 17 FLLPVYLVVLTALKEPARITLETVWQWP-HPPYWESFRTAWEA--FRPKFQNSVVLAVSA 73 +LLP+ V++T+++ ++ W WP H ++++R A F NSV++ V A Sbjct: 28 WLLPMIAVLVTSIRSSEELSEGNYWGWPKHFALFDNYREALTTSPMLHYFWNSVLITVPA 87 Query: 74 TLLSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFMKSIGLYGSLFG 133 + S + ++ G+ LA + FRG+ LFA + G F+P Q ++IP+ +G++ ++ Sbjct: 88 VIGSIALAAMAGFALAIYRFRGNSSLFATFVAGNFVPVQVLMIPVRDLSLQLGVFNTVSA 147 Query: 134 LVLVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILPLSVPAFVVVAI 193 L+L HV + L RN+ ++P ELVEAARI+GA + +F ++LPL PA +AI Sbjct: 148 LILFHVSFQTGFCALFLRNFIKQLPFELVEAARIEGANEWTVFFRIVLPLIRPALAALAI 207 Query: 194 WQFTQIWNEFLFAVTLTR-PESQPITVALAQLAGGEAVKWNLPMAGAILAALPTLLVYIL 252 FT +WN++ +A+ LT+ ++ PITV +A L G WNL AG+ILAALP++ ++ Sbjct: 208 LVFTFVWNDYFWALCLTQGDDAAPITVGVAALKGQWTTAWNLVSAGSILAALPSVAMFFA 267 Query: 253 LGRYFLRGLLAGSVKG 268 + ++F+ GL G+ KG Sbjct: 268 MQKHFVAGLTFGATKG 283 Lambda K H 0.330 0.146 0.461 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: 267 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: 268 Length of database: 283 Length adjustment: 25 Effective length of query: 243 Effective length of database: 258 Effective search space: 62694 Effective search space used: 62694 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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