Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate AZOBR_RS28565 AZOBR_RS28565 sugar ABC transporter ATPase
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__azobra:AZOBR_RS28565 Length = 602 Score = 227 bits (578), Expect = 5e-64 Identities = 124/248 (50%), Positives = 163/248 (65%), Gaps = 12/248 (4%) Query: 5 LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64 LL++ DVSK FGG+ + VG+ + +I+ LIGPNGAGK+T N++TG+ D+GT L Sbjct: 348 LLEVTDVSKAFGGVVTADKVGLRLHAHRIHALIGPNGAGKSTLINILTGVISADSGTIRL 407 Query: 65 DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124 G+ + H A GIARTFQN+RLFG MTVL+NV++G H R V G R Sbjct: 408 AGQDITRGTAHARAARGIARTFQNLRLFGSMTVLDNVLIGAHARI--GVTG--------R 457 Query: 125 EEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGM 184 EE+A + K+ +LDFVG+G+ A A L YG QRR+E+ARALA DP LL LDEPAAG+ Sbjct: 458 EEDAVAKAKA--VLDFVGLGEHAGALAGSLPYGLQRRVELARALAGDPVLLLLDEPAAGL 515 Query: 185 NATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKNP 244 N E L +L+ +I G +L++EHD+ L+M + + I VLD G IAEG P D+Q NP Sbjct: 516 NPRETAELGQLIKRIGQLGVAVLMVEHDMGLVMRISDEIVVLDRGVVIAEGAPRDIQTNP 575 Query: 245 AVIEAYLG 252 VIEAYLG Sbjct: 576 RVIEAYLG 583 Lambda K H 0.320 0.138 0.394 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: 411 Number of extensions: 20 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: 255 Length of database: 602 Length adjustment: 30 Effective length of query: 225 Effective length of database: 572 Effective search space: 128700 Effective search space used: 128700 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: 50 (23.9 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