Align histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized)
to candidate RR42_RS29645 RR42_RS29645 ABC transporter substrate-binding protein
Query= CharProtDB::CH_014295 (260 letters) >FitnessBrowser__Cup4G11:RR42_RS29645 Length = 199 Score = 206 bits (524), Expect = 3e-58 Identities = 103/190 (54%), Positives = 135/190 (71%), Gaps = 1/190 (0%) Query: 71 ENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDIQPTVES 130 +N D +IP+L+A+K DAI SS+S E+R + I FT KLYA LVV K S + T ES Sbjct: 9 KNSFDGMIPALQARKFDAINSSMSKNEQRLKVIDFTSKLYAPIEALVVKKGSPLVATAES 68 Query: 131 LKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDEVAASEG 190 LKGKRVGVLQG+TQET+ ++W G++IV YQ QD I+ DL AGRIDAA A G Sbjct: 69 LKGKRVGVLQGSTQETYARKYWGGNGVDIVPYQTQDLIWPDLIAGRIDAAMAFAPQADAG 128 Query: 191 FLKQPVGKDYKFG-GPSVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMRADGTYEKLA 249 FLK P GKD+ F GP++KD+ +FG G +G+RK+D LR+A+N A +R DGTY+K+A Sbjct: 129 FLKTPPGKDFVFAQGPAIKDDSIFGPGVSIGVRKDDTALRDAINGAIDSLRKDGTYDKIA 188 Query: 250 KKYFDFDVYG 259 KKYF+F++YG Sbjct: 189 KKYFNFNIYG 198 Lambda K H 0.315 0.133 0.372 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: 182 Number of extensions: 7 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 260 Length of database: 199 Length adjustment: 22 Effective length of query: 238 Effective length of database: 177 Effective search space: 42126 Effective search space used: 42126 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: 46 (22.3 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