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 Ac3H11_4824 Oligopeptide transport ATP-binding protein OppF (TC 3.A.1.5.1)
Query= TCDB::Q9X272 (328 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4824 Length = 295 Score = 230 bits (587), Expect = 3e-65 Identities = 114/259 (44%), Positives = 176/259 (67%), Gaps = 7/259 (2%) Query: 12 PLLQTVDLKKYFPQGKRIL-------KAVDGISIEIKEGETLGLVGESGCGKSTLGRTIL 64 PLLQ DL + + + L +A++G+S I G +LG+VGESG GKSTL R ++ Sbjct: 12 PLLQVKDLVREYTLPREHLFRPPGTVQALNGVSFSIAAGRSLGVVGESGSGKSTLARLVM 71 Query: 65 KLLRPDGGKIFFEGKDITNLNDKEMKPYRKKMQIIFQDPLGSLNPQMTVGRIIEDPLIIH 124 L P G + G+++ L ++++ R+ Q++FQDP GSL+P+ TV RI+ +PL Sbjct: 72 ALDAPTAGTVELLGRNLHQLPAEQLRQARRDFQMVFQDPYGSLDPRQTVERIVTEPLQAQ 131 Query: 125 KIGTKKERRKRVEELLDMVGIGREFINSFPHEFSGGQQQRIGIARALALNPKFIVCDEPV 184 T+ E+R++ ++L VG+ + +PHEFSGGQ+QRI IARAL P+ IV DEPV Sbjct: 132 GQTTRAEQREQAAQVLSQVGLRTNDLGKYPHEFSGGQRQRIAIARALITRPRLIVADEPV 191 Query: 185 SALDVSIQAQIIDLLEEIQQKMGISYLFIAHNLAVVEHISHKVAVMYLGKIVEYGDVDKI 244 SALDVS+QAQ+++L++++QQ+ GI+Y+ I+H+LAVV H+ +V V+Y G+IVE G ++ Sbjct: 192 SALDVSVQAQVLNLMQDLQQQFGITYMLISHDLAVVNHLCDEVVVLYQGRIVERGSPGEL 251 Query: 245 FLNPIHPYTRALLKSVPKI 263 F N HPYT++L+ +VP++ Sbjct: 252 FRNAQHPYTQSLVGAVPQV 270 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: 245 Number of extensions: 5 Number of successful extensions: 1 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: 295 Length adjustment: 27 Effective length of query: 301 Effective length of database: 268 Effective search space: 80668 Effective search space used: 80668 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