Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate GFF2789 PGA1_c28320 ABC transporter, ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Phaeo:GFF2789 Length = 255 Score = 164 bits (414), Expect = 2e-45 Identities = 86/202 (42%), Positives = 119/202 (58%) Query: 24 LQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEGPGAERGMVF 83 L + ++ V I+GPSGCGKSTLLR + GL+ T G VL G P EG VF Sbjct: 18 LSDITLDIPSGKIVCIVGPSGCGKSTLLRFIGGLERPTQGEVLQVGQPPEGCLNPLTYVF 77 Query: 84 QSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFEQHFPKQLSGGMQQR 143 Q + L PW T+ NI L + G+ A +A+ L F PKQLSGGM+QR Sbjct: 78 QDFALLPWRTVRGNISLVLEDHGIRGAAAARIIDDVLARTKLSDFAGALPKQLSGGMKQR 137 Query: 144 TAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHDIDEAIFMA 203 AIARALA +P ++LMDEP ALD+QTR L+ + L+ +W T ++VTH++ EA+ + Sbjct: 138 VAIARALAVNPAVMLMDEPLSALDSQTRELLMDDLVALWTRTPFTAVYVTHNLAEAVRLG 197 Query: 204 NRVAVFSARPGRIKTELAVDLP 225 + + V S RPG+I+ + +D P Sbjct: 198 HAIVVLSRRPGQIREIVHLDTP 219 Lambda K H 0.322 0.136 0.394 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: 171 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: 259 Length of database: 255 Length adjustment: 24 Effective length of query: 235 Effective length of database: 231 Effective search space: 54285 Effective search space used: 54285 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 (21.9 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