Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate GFF3089 HP15_3032 amino acid ABC transporter, inner membrane subunit
Query= uniprot:A0A1N7UBU2 (233 letters) >FitnessBrowser__Marino:GFF3089 Length = 247 Score = 237 bits (605), Expect = 1e-67 Identities = 122/230 (53%), Positives = 165/230 (71%), Gaps = 7/230 (3%) Query: 5 LNLHGYGPMLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRSV 64 L+L GYGP L GA +T++LAFL+LALS+ALGLI A+AKLS ++ + AT YTTLIR V Sbjct: 15 LDLKGYGPALMDGAIVTIELAFLSLALSVALGLIGASAKLSQSRVAKGIATTYTTLIRGV 74 Query: 65 PDLVLILLIFYSLQLWLNDLSEVFGWD------YFEIDPFTAGVITLGFIYGAYFTENFR 118 PDLV++LL +Y Q+ +N LS+ W+ +F+ DPF +GV+T+G I+GAY TE FR Sbjct: 75 PDLVMMLLFYYGGQVAVNMLSDYI-WEAYEIDFFFQFDPFISGVVTIGLIFGAYMTETFR 133 Query: 119 GAILSVPVGQLEAATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGL 178 GA L+V GQ+EAA AYG +R+ F ++ PQ+MR ALPGLGNNW VLLK+TALVSIIGL Sbjct: 134 GAFLAVETGQIEAARAYGFTRFHTFRRIMLPQMMRHALPGLGNNWQVLLKTTALVSIIGL 193 Query: 179 SDLVKAAQNAGKTTNEPLYFLILAGLMYLVITTLSNRVLKRLERRYNLGI 228 +D+V+ A+ A K P +F I +YL +T S +K L++R N+G+ Sbjct: 194 TDMVRVAEEAAKAERMPFHFFIPVAFVYLALTAGSELFIKWLDKRANVGV 243 Lambda K H 0.327 0.141 0.428 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: 179 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: 233 Length of database: 247 Length adjustment: 23 Effective length of query: 210 Effective length of database: 224 Effective search space: 47040 Effective search space used: 47040 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 (21.7 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