Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >NCBI__GCF_000016765.1:WP_041378948.1 Length = 252 Score = 121 bits (303), Expect = 2e-32 Identities = 79/199 (39%), Positives = 107/199 (53%), Gaps = 8/199 (4%) Query: 24 LQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPVEG-PGAER--- 79 L V + FV ++G SG GK+TLL+ + L +G + ++G V P AE Sbjct: 17 LDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIEGRDVAAQPVAELRRR 76 Query: 80 -GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRG-FEQHFPKQLS 137 G VFQ LFP +++ +N+ R +G+P ++ R A + V L F + P QLS Sbjct: 77 IGYVFQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELLDLVALPADFAERRPAQLS 136 Query: 138 GGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVLFVTHDID 197 GG QR ARALA P I+LMDEPFGALD TR + + EA T L VTHD+ Sbjct: 137 GGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRALHEAMGLTSLIVTHDMA 196 Query: 198 EAIFMANRVAVFSARPGRI 216 EA+ +A+RV V GRI Sbjct: 197 EALLLADRVIVIG--EGRI 213 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: 148 Number of extensions: 12 Number of successful extensions: 3 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: 252 Length adjustment: 24 Effective length of query: 235 Effective length of database: 228 Effective search space: 53580 Effective search space used: 53580 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 Apr 09 2024. 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