Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate AZOBR_RS29610 AZOBR_RS29610 hypothetical protein
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >FitnessBrowser__azobra:AZOBR_RS29610 Length = 221 Score = 157 bits (398), Expect = 1e-43 Identities = 89/215 (41%), Positives = 136/215 (63%), Gaps = 8/215 (3%) Query: 3 LDFSPVWAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAA 62 L++ P++A GA+ T++IT S +G +GLLVG+ R + ++ + YV Sbjct: 11 LEYWPIFA------RGAITTLQITLLSSAIGLFIGLLVGVSR-ESSGVFLRSVTSVYVEM 63 Query: 63 IRGTPLLVQLFILFFGLPQ-FGILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQME 121 IR TP LVQ+ L++ P FG L A +I LGI+SGAYVSE+VR I ++D GQ Sbjct: 64 IRATPALVQIVWLYYCFPIIFGYQLSAMTSIIIALGIHSGAYVSEIVRAGINAVDTGQFL 123 Query: 122 AARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIIS 181 AA+SIGM+ A+R ++LPQA +MIPPL NEF L+K + L S++ +++L+ E +I+ Sbjct: 124 AAKSIGMNHFTALRRIILPQAGQKMIPPLINEFANLMKLTTLGSMIAVYELLQESNNLIA 183 Query: 182 VSYRSLEVYLAIAVVYFILTGATTLVLRRIELRLR 216 +YR LEVY +A+ +FI+T + +R+E RL+ Sbjct: 184 TTYRPLEVYTFLAIFFFIITYPWIWLSQRLERRLK 218 Lambda K H 0.328 0.143 0.412 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: 140 Number of extensions: 6 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 222 Length of database: 221 Length adjustment: 22 Effective length of query: 200 Effective length of database: 199 Effective search space: 39800 Effective search space used: 39800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 45 (21.9 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