Align histidine ABC transporter, periplasmic histidine-binding protein HisJ (characterized)
to candidate H281DRAFT_06484 H281DRAFT_06484 amino acid ABC transporter substrate-binding protein, PAAT family
Query= CharProtDB::CH_018185 (260 letters) >FitnessBrowser__Burk376:H281DRAFT_06484 Length = 266 Score = 268 bits (685), Expect = 9e-77 Identities = 128/254 (50%), Positives = 180/254 (70%), Gaps = 1/254 (0%) Query: 4 LALSLSLVLAFSSATAAFAAIPQKIRIGTDPTYAPFESKNAQGELVGFDIDLAKELCKRI 63 LAL + ++ +AA A I +++R G + +YAPFESK+ GEL GFDID+ +C ++ Sbjct: 11 LALFATATATVTAGSAAAADI-KEVRFGVEASYAPFESKSPSGELQGFDIDVGNAVCAKL 69 Query: 64 NTQCTFVENPLDALIPSLKAKKIDAIMSSLSITEKRQQEIAFTDKLYAADSRLVVAKNSD 123 +C +VEN D LIP+L+A+K +AI S ++IT++R+Q + FTD +Y ++++ K S Sbjct: 70 KAKCVWVENSFDGLIPALQARKFNAINSDMTITDQRRQAVDFTDPIYTIPNQMIAKKGSG 129 Query: 124 IQPTVASLKGKRVGVLQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQD 183 + PT ASLKGK VGVLQGT QET+ WAP G+++V YQ QD IY+DL +GR+DA+FQD Sbjct: 130 LLPTPASLKGKHVGVLQGTIQETYAKARWAPAGVDVVPYQTQDQIYADLASGRLDASFQD 189 Query: 184 EVAASEGFLKQPVGKDYKFGGPAVKDEKLFGVGTGMGLRKEDNELREALNKAFAEMRADG 243 AAS+GFLK+P G ++F GPAV DEKL G G G G+RK D L++ALN+A E++ADG Sbjct: 190 AEAASKGFLKKPQGAGFEFAGPAVSDEKLLGAGVGFGIRKGDAALKDALNQALKELKADG 249 Query: 244 TYEKLAKKYFDFDV 257 T ++ A KYFD V Sbjct: 250 TIDRFAAKYFDVKV 263 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: 215 Number of extensions: 4 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: 266 Length adjustment: 25 Effective length of query: 235 Effective length of database: 241 Effective search space: 56635 Effective search space used: 56635 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