Align ABC transporter for L-Histidine, ATPase component (characterized)
to candidate Pf1N1B4_5098 Nitrate ABC transporter, ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2560 (259 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5098 Length = 263 Score = 187 bits (474), Expect = 2e-52 Identities = 108/252 (42%), Positives = 154/252 (61%), Gaps = 12/252 (4%) Query: 4 VSIQAVSRVFETAKGQRTQALQPVDFEVRDNDFVTILGPSGCGKSTLLRIVAGLDHATSG 63 V + VS+ F+T KG R QAL V+ + +FV+++G SGCGKST+L ++AGL A G Sbjct: 5 VELTQVSKHFDTKKG-RFQALSNVNLSIARGEFVSLIGHSGCGKSTVLNLIAGLLEANGG 63 Query: 64 RVLLDGAPVEGPGAERGMVFQSYTLFPWLTIEQNIR------FGLRERGMPEAQQKERAA 117 ++ +G ++GPG ER +VFQ+++L PWLT N+ FG RE +A K R Sbjct: 64 GLICNGREIDGPGPERAVVFQNHSLLPWLTCFGNVHLAVEKVFGKREN---KAALKTRTE 120 Query: 118 YFIAKVGLRGFEQHFPKQLSGGMQQRTAIARALANDPKILLMDEPFGALDNQTRVLMQEL 177 +A VGL P ++SGGM+QR IARALA +PKILLMDEPFGALD TR +Q+ Sbjct: 121 AALAMVGLEHAMHKHPSEISGGMKQRVGIARALAMEPKILLMDEPFGALDALTRAHLQDE 180 Query: 178 LLGIWEAERKTVLFVTHDIDEAIFMANRVAVFSARPGRIKTE-LAVDLPHPRH-YTIKTS 235 LL I A + TV+ VTHD+DEA+ +++R+ + + P E L+V L PR+ + Sbjct: 181 LLRIVAATQSTVVMVTHDVDEAVLLSDRIVMMTNGPAATVGEILSVGLAKPRNRLVLAND 240 Query: 236 PEFMDLKARLTE 247 PE+ + + E Sbjct: 241 PEYHRYRTTVLE 252 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: 162 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: 263 Length adjustment: 25 Effective length of query: 234 Effective length of database: 238 Effective search space: 55692 Effective search space used: 55692 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