Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate GFF1270 PGA1_c12860 putative taurine import ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Phaeo:GFF1270 Length = 279 Score = 191 bits (486), Expect = 1e-53 Identities = 105/241 (43%), Positives = 146/241 (60%), Gaps = 3/241 (1%) Query: 13 FETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSGRVLLDGAPV 72 F+T G AL+ V E+ DFV+ +GPSGCGK+T LR +A L+ T G ++++G Sbjct: 35 FQTNDGP-VHALKDVSLEINKGDFVSFIGPSGCGKTTFLRCIAALEQPTGGALMVNGMTP 93 Query: 73 EGPGAER--GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAAYFIAKVGLRGFEQ 130 + +R G VFQ+ L+PW +I +NI+ L G +A+Q R + V L GF Sbjct: 94 DEARRQRAYGYVFQAAGLYPWRSIAKNIKLPLEIMGYSKAEQAARVEQVLELVELAGFGG 153 Query: 131 HFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQELLLGIWEAERKTVL 190 +P QLSGGMQQR +IARALA D ILLMDEPFGALD R + E LL +W KT+ Sbjct: 154 KYPWQLSGGMQQRASIARALAFDADILLMDEPFGALDEIVRDHLNEQLLKLWARTDKTIG 213 Query: 191 FVTHDIDEAIFMANRVAVFSARPGRIKTELAVDLPHPRHYTIKTSPEFMDLKARLTEEIR 250 FVTH I EA++++ ++ V S RPGRI + LP R I+ S EF+++ R+ + +R Sbjct: 214 FVTHSIPEAVYLSTKIVVMSPRPGRIHDVIDSPLPKERPLDIRDSAEFIEIAHRVRDGLR 273 Query: 251 A 251 A Sbjct: 274 A 274 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: 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: 279 Length adjustment: 25 Effective length of query: 234 Effective length of database: 254 Effective search space: 59436 Effective search space used: 59436 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