Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate GFF2495 Psest_2543 ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__psRCH2:GFF2495 Length = 248 Score = 198 bits (504), Expect = 8e-56 Identities = 92/187 (49%), Positives = 135/187 (72%) Query: 30 EVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEGPGAERGMVFQSYTLF 89 E + V ++GPSGCGKSTLL +VAGL+ ++GRVL DG P+ P R +VFQ + L+ Sbjct: 24 EFAQGELVALVGPSGCGKSTLLHLVAGLEKPSAGRVLADGKPIAEPSPRRTLVFQEHALY 83 Query: 90 PWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFEQHFPKQLSGGMQQRTAIARA 149 PWL+++ N+ L +G+ ++ E+A ++ +VGL GFE ++P Q+SGGM+QRTA+ARA Sbjct: 84 PWLSLQGNVAMALELQGVAKSNAFEQAQSWLERVGLNGFEHYYPHQVSGGMRQRTALARA 143 Query: 150 LANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHDIDEAIFMANRVAVF 209 P++LL+DEPFGALD TR+ +Q++L + E + TVL VTHD+DEA+++A+ V VF Sbjct: 144 FIAKPEVLLLDEPFGALDALTRMALQDVLRELIEEHQPTVLLVTHDVDEALYLADHVLVF 203 Query: 210 SARPGRI 216 SARP R+ Sbjct: 204 SARPTRV 210 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: 189 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: 248 Length adjustment: 24 Effective length of query: 235 Effective length of database: 224 Effective search space: 52640 Effective search space used: 52640 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