Align Monocarboxylate 2-oxoacid-binding periplasmic protein all3028; Extracellular solute-binding protein; Extracytoplasmic solute receptor protein all3028; TRAP transporter monocarboxylate 2-oxoacid-binding subunit P (characterized)
to candidate GFF3941 Psest_4011 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component
Query= SwissProt::Q8YSQ6 (364 letters) >FitnessBrowser__psRCH2:GFF3941 Length = 367 Score = 320 bits (819), Expect = 5e-92 Identities = 159/364 (43%), Positives = 226/364 (62%), Gaps = 6/364 (1%) Query: 1 MKRREVLNTAAIATATTALVSCTQTNTSSV-----QAGLPNVRWRMTTSWPKSL-GTFIG 54 MKRR++L A + A TAL C + V QA W+M TSWPK+ G +G Sbjct: 1 MKRRDILTAAGVGLAATALAGCNDKSDKPVAGESKQAEQQTFNWKMVTSWPKNFPGVGVG 60 Query: 55 AETVAKRVAEMTNGRFKITPFAAGELVPGLQVLDAVQAGTVECGHTSSYYYIGKSPALAF 114 AE A V EM+ GR KI +AAGELVP L+V DAV GT E GH + YY+ GK PA F Sbjct: 61 AERFANLVNEMSGGRLKIKVYAAGELVPALEVFDAVSRGTAEMGHGAPYYWKGKVPAAQF 120 Query: 115 ATSVPFGLNAQQQYAWLYQGGGLAAIQKIYANFNVINFPAGSTGAQMGGWFKKEIKSVSD 174 ++PFG NAQ+ AWL++GGG+ +++Y + V+ G+TG Q GWF KEI SV D Sbjct: 121 FCALPFGPNAQEMNAWLHRGGGMQLWEEVYKPYGVLPMACGATGVQTAGWFNKEINSVDD 180 Query: 175 LKGLKMRIPGLGGQVMSRLGVNVQVLPGGEIYLALDRGAIDAAEWVGPYDDEKLGLNKAA 234 KGLKMR PGLGG+V++++G V +P GEI+ AL GAIDA EW+GPY+D LGL+KA+ Sbjct: 181 FKGLKMRTPGLGGEVLTKMGGTVVNMPAGEIFTALQTGAIDATEWIGPYNDLALGLHKAS 240 Query: 235 QFYYYPGWWEPGPTLDVLVNLNAWNRLPKEYQEIFKTATVEANLTMLNQYDALNGEALTR 294 ++YY PGW EP T ++ VNL AW+ LP + + I + A + N ML+ Y+A N EAL + Sbjct: 241 KYYYTPGWQEPNVTFELDVNLKAWDTLPDDLKAIVRAAARDVNGDMLDDYNAKNMEALEQ 300 Query: 295 LLAGGTKLVPYSQEIMQAAQKISFDIFEENASKDAAFKQVYEQWKAFRKQIFAWNRVNEL 354 L G ++ E++ ++++ ++ + +A D +V+EQ A+ K+++ + +NE Sbjct: 301 LREQGVEVRRLPDEVLARLKEVAAEVVDASAKADPVASKVWEQQSAYLKRLYDYAELNEK 360 Query: 355 SYEN 358 N Sbjct: 361 DIYN 364 Lambda K H 0.317 0.132 0.397 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: 464 Number of extensions: 28 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: 364 Length of database: 367 Length adjustment: 30 Effective length of query: 334 Effective length of database: 337 Effective search space: 112558 Effective search space used: 112558 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 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