Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate AO356_23510 AO356_23510 amino acid ABC transporter permease
Query= uniprot:A0A1N7UBU2 (233 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23510 Length = 229 Score = 235 bits (600), Expect = 5e-67 Identities = 114/220 (51%), Positives = 159/220 (72%) Query: 7 LHGYGPMLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRSVPD 66 L GYG ++ QGAW+T+++A A ++L LGL+ A AKLS LR+ ATLYTTL+RSVPD Sbjct: 3 LEGYGYLIFQGAWLTVQVATWAACVALVLGLLGALAKLSPLAPLRLVATLYTTLVRSVPD 62 Query: 67 LVLILLIFYSLQLWLNDLSEVFGWDYFEIDPFTAGVITLGFIYGAYFTENFRGAILSVPV 126 LVL+LLI+YS Q+ LN ++E FG + +++P+ + TLGFIYGAY E FRGA ++ Sbjct: 63 LVLMLLIYYSAQIGLNQVAEAFGRESLQLNPYGTAIGTLGFIYGAYCAETFRGAFQAIAF 122 Query: 127 GQLEAATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDLVKAAQ 186 GQLEAA AYG+S WQ + PQ+MRFALPG+GN W VLLKS L+S++GL+D+V+ A+ Sbjct: 123 GQLEAARAYGMSHWQVLRRIRLPQMMRFALPGIGNIWQVLLKSAGLISLLGLNDMVQVAK 182 Query: 187 NAGKTTNEPLYFLILAGLMYLVITTLSNRVLKRLERRYNL 226 AG T+ ++F ++ ++L LS+ VLK LERRY++ Sbjct: 183 QAGNATSRQMFFYLVIAAIFLAFAILSSLVLKHLERRYSV 222 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: 198 Number of extensions: 7 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: 229 Length adjustment: 23 Effective length of query: 210 Effective length of database: 206 Effective search space: 43260 Effective search space used: 43260 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