Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate Synpcc7942_0526 Synpcc7942_0526 ABC-type sugar transport systems permease components-like
Query= reanno::acidovorax_3H11:Ac3H11_2943 (316 letters) >FitnessBrowser__SynE:Synpcc7942_0526 Length = 293 Score = 124 bits (310), Expect = 4e-33 Identities = 83/277 (29%), Positives = 139/277 (50%), Gaps = 9/277 (3%) Query: 29 SMNRRLLPRLLLTPAMATLFLWMIVPLVMTIYFSLIR--YNLMQPDQTGFAGLENFEFFV 86 ++ RL P L L PA+ L L + P + YFS R YNL + Q + GLENF+ + Sbjct: 3 ALRDRLSPYLFLAPALTILGLTVFWPALQAFYFSFTRFDYNLTRSPQ--WVGLENFQRLL 60 Query: 87 TDPSFGTAVVNTILLLGSVILITVVLGVAIALLINEPFPGRGIVRVLLISPFFVMPTVNA 146 D F + NT + L V+ + V L + +A+L+N P G + R+ +P V V Sbjct: 61 NDAVFWKTLGNTFIYLIGVVPLLVFLPLGLAILVNRPLRGITLFRLAYYTPVIVSIVVAG 120 Query: 147 LMWKNMMMNP-IYGVLAQVWIFFGAAPVDWLTDH--PLFSVIVMVSWQWLPFATLIFMTA 203 + W+ + + L Q+ G P+ WLT LFSV+ + W+ L + +I++ Sbjct: 121 IAWRWLYAETGLLNQLGQLVFGEGFQPIPWLTSPALALFSVMAVTVWKGLGYYMVIYLAG 180 Query: 204 LQSMNHEQLEASRMDGANYLQQLRYLYVPHLGRSVAVVVMIELIFLLSIFAEIYTTTAGG 263 LQ + E EA+ +DG++ ++ + +P + + +V +I I +F E++ T GG Sbjct: 181 LQGIPLELYEAAALDGSDGWRRHLDITLPLMRPYLVLVAVISAISATKVFEEVFIMTQGG 240 Query: 264 PGDASTNVTFLIFKQALLNFDAGVASAG--ALFAVVL 298 P ++S V + +++QA + A ALF VVL Sbjct: 241 PLNSSKTVVYYVYQQAFQKLEVSYACTVGLALFLVVL 277 Lambda K H 0.331 0.142 0.436 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: 17 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: 316 Length of database: 293 Length adjustment: 27 Effective length of query: 289 Effective length of database: 266 Effective search space: 76874 Effective search space used: 76874 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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