Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate GFF148 Psest_0148 nitrate transport ATP-binding subunits C and D
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__psRCH2:GFF148 Length = 260 Score = 177 bits (449), Expect = 2e-49 Identities = 95/243 (39%), Positives = 152/243 (62%), Gaps = 6/243 (2%) Query: 1 MSSVSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHA 60 MS +SI+ + + F +Q L+ ++ + +F++I+G SGCGKST+L IVAGL Sbjct: 1 MSYLSIEHLDKSFVRGN-LASQVLKDINLNIAKGEFISIIGHSGCGKSTVLNIVAGLLDP 59 Query: 61 TSGRVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIRFGLRE---RGMPEAQQKERAA 117 + G V+LDG V GPG +R MVFQ+++L PWLT+ +N+ + + R M + +++E Sbjct: 60 SLGGVILDGKEVRGPGPDRSMVFQNHSLLPWLTVYENVEVAVNKLFKRSMNKRERREWIE 119 Query: 118 YFIAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQEL 177 + +A V + +P+++SGGM+QR IARALA PK+LL+DEPFGALD TR +Q+ Sbjct: 120 HNLALVNMGHALNKYPQEISGGMKQRVGIARALAMKPKVLLLDEPFGALDALTRAHLQDE 179 Query: 178 LLGIWEAERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTE-LAVDLPHPR-HYTIKTS 235 ++ I + T++ +THD+DEA+ +++R+ + + P E L V LP PR + Sbjct: 180 VMKIQKDLGNTMMMITHDVDEAVLLSDRIVMMTNGPSATIGEILEVKLPRPRDRIALADD 239 Query: 236 PEF 238 PE+ Sbjct: 240 PEY 242 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: 152 Number of extensions: 6 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: 260 Length adjustment: 24 Effective length of query: 235 Effective length of database: 236 Effective search space: 55460 Effective search space used: 55460 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