Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate AO353_25655 AO353_25655 amino acid ABC transporter permease
Query= uniprot:A0A1N7UBU2 (233 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25655 Length = 253 Score = 317 bits (813), Expect = 1e-91 Identities = 161/241 (66%), Positives = 190/241 (78%), Gaps = 8/241 (3%) Query: 1 MNEFLN--------LHGYGPMLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRV 52 +N FLN L GYGP+L G W+TLKL+ L+L +S+ LGL+ AAAKLS + L + Sbjct: 13 VNTFLNALGLDLSALQGYGPLLLHGTWVTLKLSALSLLVSMLLGLLGAAAKLSPLRLLNL 72 Query: 53 PATLYTTLIRSVPDLVLILLIFYSLQLWLNDLSEVFGWDYFEIDPFTAGVITLGFIYGAY 112 PAT YTTLIR VPDLVL+LLIFYSLQ WL+ L+E W Y EIDPF AG++TLGFIYGAY Sbjct: 73 PATFYTTLIRGVPDLVLMLLIFYSLQGWLSSLTEFMQWPYMEIDPFVAGIVTLGFIYGAY 132 Query: 113 FTENFRGAILSVPVGQLEAATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTAL 172 FTE FRGAILSVP GQ EA ++GLSRWQRF+ V+FPQ+MRFALP LGNNWLVLLK+TAL Sbjct: 133 FTETFRGAILSVPRGQQEAGASFGLSRWQRFYCVVFPQMMRFALPSLGNNWLVLLKATAL 192 Query: 173 VSIIGLSDLVKAAQNAGKTTNEPLYFLILAGLMYLVITTLSNRVLKRLERRYNLGIKGMA 232 VSIIGLSDLVK AQ AGK+T L FL+LA +YL+IT+ SN VL+ LERRYN G++GM Sbjct: 193 VSIIGLSDLVKVAQEAGKSTFNMLDFLLLAAALYLLITSASNYVLRVLERRYNQGVRGMT 252 Query: 233 R 233 R Sbjct: 253 R 253 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: 221 Number of extensions: 8 Number of successful extensions: 1 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: 253 Length adjustment: 23 Effective length of query: 210 Effective length of database: 230 Effective search space: 48300 Effective search space used: 48300 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