Align ATPase (characterized, see rationale)
to candidate GFF139 Psest_0139 ABC-type histidine transport system, ATPase component
Query= uniprot:Q31RN8 (261 letters) >FitnessBrowser__psRCH2:GFF139 Length = 257 Score = 229 bits (584), Expect = 4e-65 Identities = 121/243 (49%), Positives = 165/243 (67%), Gaps = 12/243 (4%) Query: 27 VEKWYGNQFQALCGVSLTVQRGEVVVMMGPSGSGKSTFLRTLNALESHQRGEIWIEGHRL 86 + K YG+ + L G+SLT + G+V+ ++G SGSGKSTFLR +N LE+ GEI + G +L Sbjct: 13 LHKRYGD-LEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHEGEILVAGEQL 71 Query: 87 -----------SHDRRDIATIRQEVGMVFQQFNLFPHLTVLQNLMLAPVQVRRWPVAQAE 135 + D + + IR E+G VFQ FNL+PH+T+L N++ AP +V A+A Sbjct: 72 KLKRDKQGDLVAADGKQLNRIRSELGFVFQNFNLWPHMTILDNIIEAPRRVLGQSKAEAT 131 Query: 136 ATARQLLERVRIAEQADKYPGQLSGGQQQRVAIARALAMQPRILLFDEPTSALDPEMVRE 195 A LL +V IA++ YP QLSGGQQQR AIAR LAMQP+++LFDEPTSALDPEMV+E Sbjct: 132 EVAEALLAKVGIADKRHVYPNQLSGGQQQRAAIARTLAMQPKVILFDEPTSALDPEMVQE 191 Query: 196 VLDVMRDLASEGMTMLVATHEVGFAREVADRVVLMADGQIVEEAPPDRFFTAPQSDRAKQ 255 VL V+R LA EG TML+ THE+ FA++V+ VV + G + E+ P++ F PQS R KQ Sbjct: 192 VLAVIRSLAEEGRTMLLVTHEMNFAKQVSSEVVFLHQGLVEEQGTPEQVFDNPQSARCKQ 251 Query: 256 FLA 258 F++ Sbjct: 252 FMS 254 Lambda K H 0.321 0.134 0.387 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: 198 Number of extensions: 8 Number of successful extensions: 2 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: 261 Length of database: 257 Length adjustment: 24 Effective length of query: 237 Effective length of database: 233 Effective search space: 55221 Effective search space used: 55221 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