Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate Ac3H11_2554 Amino acid ABC transporter, permease protein
Query= uniprot:A0A1N7UBU2 (233 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2554 Length = 222 Score = 107 bits (266), Expect = 2e-28 Identities = 68/217 (31%), Positives = 110/217 (50%), Gaps = 12/217 (5%) Query: 12 PMLAQGAWMTLKLAFLALALSLALGLIAAAAKLS-SAKWLRVPATLYTTLIRSVPDLVLI 70 P L GA +T+++ +L L +GL+ +L+ + + T Y IR P LV + Sbjct: 13 PQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQL 72 Query: 71 LLIFYSLQLWLNDLSEVFGWDYFEIDPFTAGVITLGFIYGAYFTENFRGAILSVPVGQLE 130 ++F+ L FG + F GVI LG GAY +E RGAI S+ GQ+E Sbjct: 73 FILFFGLPQ--------FG---ILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQME 121 Query: 131 AATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDLVKAAQNAGK 190 AA + G+S V+ PQ + +P LGN ++ L+K++ALVS++ + DL+ Q Sbjct: 122 AARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIIS 181 Query: 191 TTNEPLYFLILAGLMYLVITTLSNRVLKRLERRYNLG 227 + L + ++Y ++T + VL+R+E R G Sbjct: 182 VSYRSLEVYLAIAVVYFILTGATTLVLRRIELRLRAG 218 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: 117 Number of extensions: 4 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: 222 Length adjustment: 22 Effective length of query: 211 Effective length of database: 200 Effective search space: 42200 Effective search space used: 42200 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