Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate GFF1302 PGA1_c13180 ABC transporter, ATP binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__Phaeo:GFF1302 Length = 334 Score = 151 bits (381), Expect = 2e-41 Identities = 82/214 (38%), Positives = 125/214 (58%), Gaps = 8/214 (3%) Query: 1 MSSVSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHA 60 M + +++V++ F + + P+D + D +F +GPSGCGKSTLLR++AGL+ Sbjct: 1 MGQIKLESVTKNFGPV-----EVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDI 55 Query: 61 TSGRVLLDGAPVEG-PGAERG--MVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQKERAA 117 TSG + +DG P A+RG MVFQSY L+P +++ +NI F ++ G+P +QK R Sbjct: 56 TSGTIRIDGEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRID 115 Query: 118 YFIAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQEL 177 A + L + P QLSGG +QR AI RA+ +P L DEP LD RV M+ Sbjct: 116 NAAAALNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLE 175 Query: 178 LLGIWEAERKTVLFVTHDIDEAIFMANRVAVFSA 211 + + + T+++VTHD EA+ MA+++ V A Sbjct: 176 ISELHKRLATTMIYVTHDQVEAMTMADKIVVLQA 209 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: 187 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: 259 Length of database: 334 Length adjustment: 26 Effective length of query: 233 Effective length of database: 308 Effective search space: 71764 Effective search space used: 71764 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