Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate HSERO_RS08240 HSERO_RS08240 sulfate ABC transporter ATP-binding protein
Query= reanno::pseudo5_N2C3_1:AO356_09610 (276 letters) >FitnessBrowser__HerbieS:HSERO_RS08240 Length = 359 Score = 169 bits (429), Expect = 6e-47 Identities = 87/231 (37%), Positives = 138/231 (59%), Gaps = 10/231 (4%) Query: 43 GCVVGVNDLSLSIGTGEIFVIMGLSGSGKSTLVRHFNRLIDPTSGAILVDGEDILQLDMD 102 G +ND+SL+ GE+ ++G SG GK+TL+R L P SG +L+DGED Sbjct: 13 GSFTALNDVSLNFPAGELTALLGPSGCGKTTLLRIIAGLESPDSGQVLLDGEDA------ 66 Query: 103 ALREFRRHKISMVFQSFGLLPHKSVLDNVAYGLKVRGESKQ----VCAERALHWINTVGL 158 + R R ++ VFQ + L H +V +N+A+GL+V+ S++ V E+ + V L Sbjct: 67 SARHVRERQVGFVFQHYALFKHMTVFENIAFGLRVKPRSQRPSEAVIREKVKRLLELVQL 126 Query: 159 KGYENKYPHQLSGGMRQRVGLARALAADTDIILMDEAFSALDPLIRAEMQDQLLELQKTL 218 ++YP QLSGG RQR+ LARALA + ++L+DE F ALD +R E++ L L L Sbjct: 127 DWLADRYPPQLSGGQRQRIALARALAVEPRVLLLDEPFGALDAKVRKELRRWLRRLHDEL 186 Query: 219 HKTIVFITHDLDEAVRIGNRIAILKDGKLIQVGTPREILHSPADEYVDRFV 269 H T +F+THD +EA+ + +++ ++ G++ Q+GTP + + PA +V F+ Sbjct: 187 HVTSIFVTHDQEEALEVADQVVLMNKGQVEQIGTPEAVYNHPASPFVYGFL 237 Lambda K H 0.321 0.138 0.387 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: 249 Number of extensions: 14 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: 276 Length of database: 359 Length adjustment: 27 Effective length of query: 249 Effective length of database: 332 Effective search space: 82668 Effective search space used: 82668 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 (21.9 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