Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate H281DRAFT_05890 H281DRAFT_05890 carbohydrate ABC transporter membrane protein 2, CUT1 family
Query= uniprot:D8IPH9 (270 letters) >FitnessBrowser__Burk376:H281DRAFT_05890 Length = 317 Score = 154 bits (388), Expect = 3e-42 Identities = 97/282 (34%), Positives = 131/282 (46%), Gaps = 34/282 (12%) Query: 15 IVLVLVAVFPLLWALLNSVKTLLDIVTPTPRFLFTPTLENY--------RQ--------- 57 I L+A+ P+LW L S KT D + P LF P++E Y RQ Sbjct: 26 ITYALIAILPILWICLTSFKTQEDAIAYPPVVLFQPSMEGYVNLFTIRSRQTPEFIASLP 85 Query: 58 ----------------VIGSPEVLVGLTNSAVIVGSAVLLGTFMGVPAAYVIARYHVPGK 101 + G +VL NS VI + L F+G AAY +R+ VP Sbjct: 86 PAQTWYERDVRKRNMVIAGPSKVLPRFVNSLVIGFGSTFLAVFLGTLAAYAFSRFKVPLA 145 Query: 102 RDIQFFLLSLRFLPPVAVAIPLIAIWVDLGLYDTRFSMIVTYLLTTLSTITWLSIPVFQR 161 D+ FF+LS R +PP+AVAIP+ ++ LGL D+ MIV Y +S WL Sbjct: 146 DDLLFFILSTRMMPPIAVAIPIYLMYRALGLSDSYVGMIVLYTAVNVSLAVWLLKGFMDE 205 Query: 162 MPREIEEAATLDGYGPYAVFWKIALPNCATTLLGGIIFSFVLVWNELMIALALTSSNSAT 221 +PRE EEAA +DGY F K+ LP T + IF + WNE A LTS ++ T Sbjct: 206 IPREYEEAALVDGYTRLQAFVKVVLPQAITGIAATAIFCLIFAWNEYAFASLLTSGDAQT 265 Query: 222 LPVVASAFTSMGQEVPWGVINASTVLLALPPLIFVGVLSRLL 263 +P G + W + A+T L +P LIF VL + L Sbjct: 266 MPPFIPFIIGEGGQ-DWPAVAAATTLFVVPILIFTVVLRKHL 306 Lambda K H 0.327 0.142 0.434 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: 232 Number of extensions: 8 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 270 Length of database: 317 Length adjustment: 26 Effective length of query: 244 Effective length of database: 291 Effective search space: 71004 Effective search space used: 71004 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 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