Align ABC transporter for L-Histidine, permease component 2 (characterized)
to candidate HSERO_RS01860 HSERO_RS01860 sulfonate ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_2561 (252 letters) >FitnessBrowser__HerbieS:HSERO_RS01860 Length = 273 Score = 134 bits (338), Expect = 1e-36 Identities = 78/262 (29%), Positives = 134/262 (51%), Gaps = 17/262 (6%) Query: 4 RARWMLGLAFFVVFVAVWAFFTLGGFVSPTFLASPITMAKE----------------GWL 47 + ++ GL ++ +A+W + G+++P L SP + ++ WL Sbjct: 6 KGSFLQGLLVPIIVIALWEGASRAGWINPQILPSPWAVLRKWVEYATPLKPYDPEAGSWL 65 Query: 48 LFTEYG-FIKDIGMTIWRVVGGFVLAAVIAVPLGIAMGAYKGIEAFFEPFISFCRYLPAS 106 + G + D +++RVV GF++ A +A+PLG+ MG+ + I + R +P Sbjct: 66 AWAFSGELVMDAIGSLYRVVAGFLIGAGLALPLGLLMGSSQRIYGLMNLTVQVIRPIPPI 125 Query: 107 AFIPLLILWAGIGEAQKILVIFIGSVFQITLMVAVTVGGARRDLVEAAYTLGAGHKGIVT 166 A+IPL ILW G+G + +I +G+ F + + V + AA LGA + Sbjct: 126 AYIPLAILWFGLGNPPALFLISLGAFFPVLMNTIAGVRQVDSIYLRAARNLGASQSTLFL 185 Query: 167 RVLIPGAAPEIAETLRLVLGWAWTYVIVAELIGSSSGIGHMITDSQSLLNTGQIIFGIII 226 RV++P A P I +R+ +G A+ VIVAE+I S+G+G I +++ + +II G+I Sbjct: 186 RVMLPAAVPYILSGVRIGIGTAFIVVIVAEMIAVSNGLGFRIMEAREYFWSDKIIAGMIT 245 Query: 227 IGLIGLVSDFAFKALNHRLFAW 248 IGL+GL D LN+ + W Sbjct: 246 IGLLGLAIDLGMSRLNNYMLRW 267 Lambda K H 0.331 0.145 0.456 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: 221 Number of extensions: 12 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: 252 Length of database: 273 Length adjustment: 25 Effective length of query: 227 Effective length of database: 248 Effective search space: 56296 Effective search space used: 56296 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: 47 (22.7 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