Align Histidine transport ATP-binding protein HisP (characterized)
to candidate H281DRAFT_00221 H281DRAFT_00221 amino acid ABC transporter ATP-binding protein, PAAT family
Query= SwissProt::P02915 (258 letters) >FitnessBrowser__Burk376:H281DRAFT_00221 Length = 259 Score = 355 bits (912), Expect = e-103 Identities = 172/256 (67%), Positives = 217/256 (84%) Query: 3 SENKLHVIDLHKRYGGHEVLKGVSLQARAGDVISIIGSSGSGKSTFLRCINFLEKPSEGA 62 ++ KL V +LHK+YG +EVLKGV+L+A AGDVIS+IGSSGSGKST LRCINFLE+P+ G Sbjct: 4 TKQKLFVDELHKQYGDNEVLKGVTLKANAGDVISVIGSSGSGKSTMLRCINFLEQPNAGR 63 Query: 63 IIVNGQNINLVRDKDGQLKVADKNQLRLLRTRLTMVFQHFNLWSHMTVLENVMEAPIQVL 122 I V+G+ + K+G L+V+D QL+ +RT+L+MVFQHFNLWSHM VLEN++EAP+ VL Sbjct: 64 IFVDGEEVRTQIAKNGALRVSDPKQLQRVRTKLSMVFQHFNLWSHMNVLENIVEAPVNVL 123 Query: 123 GLSKHDARERALKYLAKVGIDERAQGKYPVHLSGGQQQRVSIARALAMEPDVLLFDEPTS 182 GL + +A +RA +YL KVG+ R + +YP HLSGGQQQRV+IARALAM PDV+LFDEPTS Sbjct: 124 GLKRKEAEDRAREYLEKVGLAPRLEKQYPSHLSGGQQQRVAIARALAMHPDVMLFDEPTS 183 Query: 183 ALDPELVGEVLRIMQQLAEEGKTMVVVTHEMGFARHVSSHVIFLHQGKIEEEGDPEQVFG 242 ALDPELVGEVL++MQ LAEEG+TM+VVTHEM FAR+VS+HV+FLHQG++EEEG P++VF Sbjct: 184 ALDPELVGEVLKVMQTLAEEGRTMIVVTHEMAFARNVSNHVMFLHQGRVEEEGHPDEVFR 243 Query: 243 NPQSPRLQQFLKGSLK 258 N +S RL+QFL GSLK Sbjct: 244 NTRSERLKQFLSGSLK 259 Lambda K H 0.319 0.136 0.383 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: 239 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: 258 Length of database: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 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 (21.7 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