Align Solute-binding protein Bpro_3107 (characterized)
to candidate Ac3H11_2073 TRAP-type C4-dicarboxylate transport system, periplasmic component
Query= SwissProt::Q128M1 (330 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2073 Length = 328 Score = 160 bits (406), Expect = 3e-44 Identities = 104/327 (31%), Positives = 168/327 (51%), Gaps = 4/327 (1%) Query: 1 MTNRTPRISAIRSAALAALLAGLGMGAAQATEFRSADTHNADDYPTVAAVKYMGELLEKK 60 M +T + + +AALA L GL AQA + + AAVK+ E L+ K Sbjct: 1 MQRKTFTRTLLAAAALAVALPGLAQ--AQAMKLTLGHGAAPGNPRHEAAVKF-AETLKAK 57 Query: 61 SGGKHKIKVFNKQALGSEKETIDQVKIGALDFTRVNVGPMNAICPLTQVPTMPFLFSSIA 120 + G+ +++V LG + + V+ GALD T + G ++ P MPF+FS+ A Sbjct: 58 TAGRIEVQVAPSAQLGDDAAMVTAVRTGALDMTANSQGAVSVAVPEYAAYGMPFMFSTPA 117 Query: 121 HMRKSLDGPVGDEILKSCESAGFIGLAFYDSGARSIY-AKKPIRTVADAKGLKIRVQQSD 179 K LDGP+G E+ + G + L ++D+G R + +K+PI V D KGLK+R Sbjct: 118 QAFKLLDGPLGQELAQKSADKGMVVLGYWDNGIRHMTNSKRPITKVEDMKGLKMRTPPDA 177 Query: 180 LWVALVSAMGANATPMPYGEVYTGLKTGLIDAAENNIPSFDTAKHVEAVKVYSKTEHSMA 239 + V ++ A+GA A + + E+Y L+ G++D EN + + +K E K + T H Sbjct: 178 VLVDIMQALGAEAQQIKFAELYVALQQGVVDGQENPLVNIHASKLYEVQKHLALTSHMFQ 237 Query: 240 PEILVMSKIIYDKLPKAEQDMIRAAAKESVAFERQKWDEQEAKSLANVKAAGAEIVEVDK 299 +MSK +D+L A++ + AA E+ A +R+ E + K L ++KA G ++ VDK Sbjct: 238 MTPFLMSKRTWDRLSDADRKAVTEAAAEATALQRKMSQEADDKLLDDLKAKGVQVTTVDK 297 Query: 300 KSFQAVMGPVYDKFMTTPDMKRLVKAV 326 +F V K++TTP L K + Sbjct: 298 AAFAKATAAVDAKWLTTPIGPYLKKVI 324 Lambda K H 0.316 0.130 0.362 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: 206 Number of extensions: 10 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: 330 Length of database: 328 Length adjustment: 28 Effective length of query: 302 Effective length of database: 300 Effective search space: 90600 Effective search space used: 90600 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 (21.6 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