Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate WP_052668647.1 NITAL_RS23120 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWL6 (233 letters) >NCBI__GCF_000969705.1:WP_052668647.1 Length = 231 Score = 187 bits (474), Expect = 2e-52 Identities = 100/232 (43%), Positives = 146/232 (62%), Gaps = 3/232 (1%) Query: 1 MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60 ML+ ++++ Y + L VN+ V G +++L+G NG GK+T + T+ G +GSIR+ Sbjct: 1 MLEVQDLAGGYPGTRVLDGVNLSVADGAVLSLLGRNGVGKTTFVHTIMGMLPG-TGSIRF 59 Query: 61 MGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTDKGDYQEQMDKVLHLF 120 GEEL+G+ + I R +A+VP+GRRVF LTVEENL + G + + V LF Sbjct: 60 AGEELIGRSTYQIARAGLALVPQGRRVFGPLTVEENLQIAARNARPGKWTPE--SVYELF 117 Query: 121 PRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQLR 180 P+L +R RG +SGGEQ+ML+IGRAL++ P+LLLLDEPS GLAP I+ + D++ L Sbjct: 118 PQLADRRANRGSVLSGGEQEMLSIGRALVTNPRLLLLDEPSDGLAPSIVNLVGDVVRSLA 177 Query: 181 KDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232 +GVT+ LVEQN AL++A V+ GR+ +G E L +D + LG Sbjct: 178 SEGVTILLVEQNVALALRVATETAVMSKGRITFRGNPEELRSDDGLVRDLLG 229 Lambda K H 0.320 0.137 0.381 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: 176 Number of extensions: 7 Number of successful extensions: 3 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: 231 Length adjustment: 23 Effective length of query: 210 Effective length of database: 208 Effective search space: 43680 Effective search space used: 43680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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