Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate 3607963 Dshi_1371 ABC transporter related (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Dino:3607963 Length = 333 Score = 203 bits (516), Expect = 4e-57 Identities = 113/250 (45%), Positives = 156/250 (62%), Gaps = 3/250 (1%) Query: 4 VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63 +S + + VF+T G AL V+ E+ +FV+ +GPSGCGK+T LR VAGL+H T G Sbjct: 80 ISARDLDLVFQTNDGP-VHALSGVNLEIGKGEFVSFIGPSGCGKTTFLRAVAGLEHPTGG 138 Query: 64 RVLLDG-APVEGPGAER-GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIA 121 + ++G P E A G VFQ+ L+PW TI +NI L+ G +A Q+ R A + Sbjct: 139 SLTVNGMTPDEARQARAYGYVFQAAGLYPWRTIAKNISLPLQIMGYSKADQEARVARVLE 198 Query: 122 KVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGI 181 V L GF + +P QLSGGMQQR +IARAL+ D ILLMDEPFGALD R + E LL + Sbjct: 199 LVELSGFAKKYPWQLSGGMQQRASIARALSFDADILLMDEPFGALDEIVRDHLNEQLLAL 258 Query: 182 WEAERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTELAVDLPHPRHYTIKTSPEFMDL 241 W+ KT+ FVTH I EA++++ ++ V S RPGRI + LP R I+ +PEF+++ Sbjct: 259 WKRTEKTIGFVTHSIPEAVYLSTKIVVMSPRPGRITDVIDSPLPLDRPLDIRDTPEFIEI 318 Query: 242 KARLTEEIRA 251 R+ E +RA Sbjct: 319 AHRVREGLRA 328 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: 233 Number of extensions: 4 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: 259 Length of database: 333 Length adjustment: 26 Effective length of query: 233 Effective length of database: 307 Effective search space: 71531 Effective search space used: 71531 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: 48 (23.1 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