Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate 5210215 Shew_2658 ABC transporter-related protein (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__PV4:5210215 Length = 227 Score = 141 bits (355), Expect = 1e-38 Identities = 76/216 (35%), Positives = 124/216 (57%), Gaps = 10/216 (4%) Query: 3 SVSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATS 62 +++IQA+++++ A++ +D + +FV I+GPSG GK+TLL ++ G+D +S Sbjct: 2 TIAIQALTKIYNPESDFPVAAVKSLDLTIAQGEFVAIMGPSGSGKTTLLNMIGGIDSPSS 61 Query: 63 GRVLLDGAPVEGPGAER---------GMVFQSYTLFPWLTIEQNIRFGLRERGMPEAQQK 113 G V +DG + + G +FQ Y+L P LT +N+ F ++ +G EA+ + Sbjct: 62 GAVFIDGEDITHLSEQALIAFRRDHVGFIFQDYSLLPVLTALENVEFVMQLQGHSEAECR 121 Query: 114 ERAAYFIAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVL 173 +RA +A+VGL + P +LSGG QQR A+ARALA P+ ++ DEP LD ++ Sbjct: 122 DRAMALLAQVGLAAQQDKIPAKLSGGQQQRVAVARALAPRPRFVMADEPTANLDAKSTAE 181 Query: 174 MQELLLGIWEAERKTVLFVTHDIDEAIFMANRVAVF 209 + +++ + E E T +F THD I A RV VF Sbjct: 182 LLDIMQSLNEQEGTTFIFSTHD-PRVIARAKRVIVF 216 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: 136 Number of extensions: 7 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: 227 Length adjustment: 23 Effective length of query: 236 Effective length of database: 204 Effective search space: 48144 Effective search space used: 48144 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: 46 (22.3 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