Align ABC transporter permease subunit; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine transport system permease protein (characterized, see rationale)
to candidate WP_092487756.1 BM299_RS18040 amino acid ABC transporter permease
Query= uniprot:A0A1N7UBU2 (233 letters) >NCBI__GCF_900115975.1:WP_092487756.1 Length = 234 Score = 132 bits (332), Expect = 6e-36 Identities = 76/223 (34%), Positives = 120/223 (53%), Gaps = 8/223 (3%) Query: 13 MLAQGAWMTLKLAFLALALSLALGLIAAAAKLSSAKWLRVPATLYTTLIRSVPDLVLILL 72 ++ QGA +TL++ +++A+ LGLI ++LS K LR AT Y R P LV I + Sbjct: 11 LIFQGAKITLQITIISVAIGCLLGLIGGLSRLSRRKVLRFLATAYVDFFRGTPLLVQIFI 70 Query: 73 IFYSLQLWLNDLS----EVFGW----DYFEIDPFTAGVITLGFIYGAYFTENFRGAILSV 124 +++ + L DL + +G D F + F A VI GAY E FR + S+ Sbjct: 71 VYFGIPKLLMDLQSFMVDSYGMTPVADSFALPRFLAAVIACSLNSGAYVAEIFRAGVQSI 130 Query: 125 PVGQLEAATAYGLSRWQRFHLVLFPQLMRFALPGLGNNWLVLLKSTALVSIIGLSDLVKA 184 GQ+EAA + G++ Q V+ PQ + +P LGN ++ +LK T+L+S+IG ++L + Sbjct: 131 ERGQMEAARSLGMTHGQAMRYVILPQAFKRVIPPLGNEFIAMLKDTSLLSVIGFAELTRN 190 Query: 185 AQNAGKTTNEPLYFLILAGLMYLVITTLSNRVLKRLERRYNLG 227 Q T E + G +YL++T +R++ LERRY G Sbjct: 191 GQLIIARTYESFAIWLTVGFIYLIMTFTLSRIVDYLERRYKTG 233 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: 122 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: 234 Length adjustment: 23 Effective length of query: 210 Effective length of database: 211 Effective search space: 44310 Effective search space used: 44310 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 Apr 09 2024. 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