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 WP_134789831.1 BIBO1_RS17965 carbohydrate ABC transporter permease
Query= TCDB::Q72KX4 (268 letters) >NCBI__GCF_000182725.1:WP_134789831.1 Length = 274 Score = 131 bits (329), Expect = 2e-35 Identities = 82/254 (32%), Positives = 135/254 (53%), Gaps = 6/254 (2%) Query: 18 LLPVYLVVLTALKEPARITLETVWQWPHPPYWESFRTAWEA--FRPKFQNSVVLAVSATL 75 L P ++ LTA+K PA+ L W WP W++F W A F NS+ ++V A++ Sbjct: 23 LFPFAVMFLTAVK-PAQEVLSPNW-WPSTFRWQNFSEMWVATNFGNALLNSIYVSVIASV 80 Query: 76 LSALVGSLNGYVLAKWPFRGSGLLFALILFGMFIPYQSILIPLFQFMKSIGLYGSLFGLV 135 + ++ Y ++++ F G +L I +++ LF+ + + GL S+ + Sbjct: 81 GAIIISIPAAYAMSRFRFAAHGAFRQFLLVSQMISPIVLVLGLFRLLAAYGLIESVSAVG 140 Query: 136 LVHVIYGIPIVTLIFRNYYSEIPDELVEAARIDGAGFFGIFRHVILPLSVPAFVVVAIWQ 195 V++ + I + ++Y+ IP +L EA+ ++GAG V LPL +PA V AI+ Sbjct: 141 AVYMAFNIAFTVWMLQSYFDTIPRDLEEASWMEGAGRGKTLVKVFLPLCLPAIAVTAIFT 200 Query: 196 FTQIWNEFLFAVT-LTRPESQPITVALAQL-AGGEAVKWNLPMAGAILAALPTLLVYILL 253 F WNEF+ A+T L R ES + + + L AG V+W+ MA LA LP +++I L Sbjct: 201 FINAWNEFVVALTMLRRQESYTLPIQVFSLVAGRYTVEWHYVMAATFLATLPVAILFIWL 260 Query: 254 GRYFLRGLLAGSVK 267 RY ++GL G+VK Sbjct: 261 QRYLIKGLALGAVK 274 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: 219 Number of extensions: 15 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: 268 Length of database: 274 Length adjustment: 25 Effective length of query: 243 Effective length of database: 249 Effective search space: 60507 Effective search space used: 60507 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 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