Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate Pf1N1B4_4792 Histidine ABC transporter, permease protein HisQ (TC 3.A.1.3.1)
Query= uniprot:A0A1N7UBU2 (233 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4792 Length = 371 Score = 320 bits (821), Expect = 2e-92 Identities = 163/238 (68%), Positives = 190/238 (79%), Gaps = 8/238 (3%) Query: 1 MNEFLNL--------HGYGPMLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRV 52 +N FLNL GYGP+L G W+TLKL+ L+L +S+ALGL+ AAAKLS K L + Sbjct: 1 VNSFLNLIGVDLSSLQGYGPLLLHGTWVTLKLSALSLLVSMALGLLGAAAKLSPLKLLNL 60 Query: 53 PATLYTTLIRSVPDLVLILLIFYSLQLWLNDLSEVFGWDYFEIDPFTAGVITLGFIYGAY 112 PAT YTTLIR VPDLVL+LLIFYSLQ WL+ L+E W Y EIDPF AGV+TLGFIYGAY Sbjct: 61 PATFYTTLIRGVPDLVLMLLIFYSLQGWLSSLTEAMDWPYMEIDPFVAGVVTLGFIYGAY 120 Query: 113 FTENFRGAILSVPVGQLEAATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTAL 172 FTE FRGAILSVP GQ EAA ++GL+RWQRF V+FPQ+MRFALP LGNNWLVLLK+TAL Sbjct: 121 FTETFRGAILSVPRGQQEAAASFGLNRWQRFRFVVFPQMMRFALPSLGNNWLVLLKATAL 180 Query: 173 VSIIGLSDLVKAAQNAGKTTNEPLYFLILAGLMYLVITTLSNRVLKRLERRYNLGIKG 230 VSIIGLSDLVK AQ AGK+T L FL+LAG +YL+IT+ SN VL+ LERRYN G++G Sbjct: 181 VSIIGLSDLVKVAQEAGKSTFNMLDFLLLAGALYLLITSASNYVLRVLERRYNQGVRG 238 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: 264 Number of extensions: 10 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: 371 Length adjustment: 26 Effective length of query: 207 Effective length of database: 345 Effective search space: 71415 Effective search space used: 71415 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: 48 (23.1 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