Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate WP_052669757.1 NITAL_RS17070 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWL6 (233 letters) >NCBI__GCF_000969705.1:WP_052669757.1 Length = 245 Score = 195 bits (495), Expect = 8e-55 Identities = 106/235 (45%), Positives = 149/235 (63%), Gaps = 4/235 (1%) Query: 1 MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60 +L+ V + YG + LH V++++ +G L G NGAGK+T M +CG+ +G+I + Sbjct: 13 LLRLTGVRSGYGPLPVLHGVDLDIEEGRTAVLFGLNGAGKTTTAMNICGALSTWAGTIEF 72 Query: 61 MGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTDK-GDY-QEQMDKVLH 118 G+++ + + I +VPEGRRVF LTVE NL +G + + GD+ EQ + VL Sbjct: 73 DGQDVTRWSTKRCVDAGIVMVPEGRRVFPDLTVERNLQVGSWSQRRDGDWVAEQREIVLD 132 Query: 119 LFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQ 178 FPRL+ER Q GT+SGGEQQMLAI R LM++PKLL++DE S+GLAP+I++ +FDI+ Sbjct: 133 YFPRLRERLEQLAGTLSGGEQQMLAIARGLMARPKLLIIDEASMGLAPVIVKDVFDIVRA 192 Query: 179 LRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLGG 233 + DGVTV L+EQN AL +AD V+ G +V TG A LTD V L G Sbjct: 193 INADGVTVLLIEQNVG-ALDVADLGVVMAQGSIVRTLTG-AELTDRSVVSRLLMG 245 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: 134 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: 245 Length adjustment: 23 Effective length of query: 210 Effective length of database: 222 Effective search space: 46620 Effective search space used: 46620 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