Align TM1750, component of Probable mannose/mannoside porter. Induced by beta-mannan (Conners et al., 2005). Regulated by mannose-responsive regulator manR (characterized)
to candidate SMa1370 SMa1370 ABC transporter ATP-binding protein
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__Smeli:SMa1370 Length = 327 Score = 282 bits (721), Expect = 9e-81 Identities = 145/296 (48%), Positives = 199/296 (67%), Gaps = 2/296 (0%) Query: 27 KRILKAVDGISIEIKEGETLGLVGESGCGKSTLGRTILKLLRPDGGKIFFEGKDITNLND 86 +R + AV +S ++ GETLGLVGESG GK+T+GR +L+ + G+I F G+DIT+L Sbjct: 27 RRSVNAVSDVSFDLAPGETLGLVGESGSGKTTVGRAVLRRIPAAQGRIVFGGEDITHLGG 86 Query: 87 KEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIHKIGTK-KERRKRVEELLDMVGI 145 + ++ R +MQI+ QDP SLNP+M V I+ +PLI+H + +E R V ELL+ VG+ Sbjct: 87 EPLRRLRARMQIVLQDPYTSLNPRMKVSSIVAEPLIVHGLAASAEEARAAVAELLERVGL 146 Query: 146 GREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPVSALDVSIQAQIIDLLEEIQQK 205 + + +PH FSGGQ+QRIGIARALAL P IV DEPVSALDVS++AQ+++L++++Q+ Sbjct: 147 PGDAADRYPHSFSGGQRQRIGIARALALKPALIVADEPVSALDVSVRAQVVNLMQDLQRD 206 Query: 206 MGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKIFLNPIHPYTRALLKSVPKI-P 264 +GISYLFIAH+LA+V HISH+VA+MY G+IVE D I+ PIHPYT ALL +VP P Sbjct: 207 LGISYLFIAHDLAIVRHISHRVAIMYAGRIVEIAPRDAIYQRPIHPYTEALLSAVPVANP 266 Query: 265 WDGQKQRFYSLKGELPSPIDLPKGCRFQTRCTEKKAICFEKEPELTEVEKNHFVSC 320 + +R GE P GCRF RC C E+ P+L +HF +C Sbjct: 267 KLQRARRRIVPPGESVDIASPPTGCRFHPRCPLATDRCREEAPQLLRKTGDHFAAC 322 Lambda K H 0.321 0.142 0.417 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: 311 Number of extensions: 10 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: 328 Length of database: 327 Length adjustment: 28 Effective length of query: 300 Effective length of database: 299 Effective search space: 89700 Effective search space used: 89700 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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