Align histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized)
to candidate BPHYT_RS07735 BPHYT_RS07735 ABC transporter substrate-binding protein
Query= CharProtDB::CH_018185 (260 letters) >FitnessBrowser__BFirm:BPHYT_RS07735 Length = 264 Score = 269 bits (688), Expect = 4e-77 Identities = 129/253 (50%), Positives = 180/253 (71%), Gaps = 1/253 (0%) Query: 5 ALSLSLVLAFSSATAAFAAIPQKIRIGTDPTYAPFESKNAQGELVGFDIDLAKELCKRIN 64 AL+L + ++ TAA A I +++ G + +YAPFESK+ GEL GFDID+ +C ++ Sbjct: 10 ALALFAAASATAGTAAAADI-KEVHFGVEASYAPFESKSPSGELQGFDIDVGNAVCAKLK 68 Query: 65 TQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSDI 124 +C +VEN D LIP+L+A+K +AI S ++IT++R+Q + FTD +Y ++++ K S + Sbjct: 69 AKCVWVENSFDGLIPALQARKFNAINSDMTITDQRRQAVDFTDPIYTIPNQMIAKKGSGL 128 Query: 125 QPTVASLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQDE 184 PT ASLKGK VGVLQGT QET+ WAP G+++V YQ QD IY+DL +GR+DAAFQD Sbjct: 129 LPTPASLKGKHVGVLQGTIQETYAKARWAPAGVDVVPYQTQDQIYADLASGRLDAAFQDA 188 Query: 185 VAASEGFLKQPVGKDYKFGGPAVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMRADGT 244 AAS+GFLK+P G ++F GPAV DEKL G G G G+RK D L++ALN+A E++ADGT Sbjct: 189 EAASKGFLKKPQGAGFEFAGPAVTDEKLLGAGVGFGVRKGDKALKDALNQALKELKADGT 248 Query: 245 YEKLAKKYFDFDV 257 ++ A KYFD V Sbjct: 249 IDRFAAKYFDVKV 261 Lambda K H 0.316 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: 214 Number of extensions: 5 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: 260 Length of database: 264 Length adjustment: 25 Effective length of query: 235 Effective length of database: 239 Effective search space: 56165 Effective search space used: 56165 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: 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