Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate PfGW456L13_84 Urea ABC transporter, ATPase protein UrtD
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_84 Length = 290 Score = 137 bits (346), Expect = 2e-37 Identities = 90/250 (36%), Positives = 141/250 (56%), Gaps = 9/250 (3%) Query: 4 TLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTG-TF 62 T+L + D+S F G +ALN + + I G++ +IGPNGAGKTT +VITG +P G + Sbjct: 48 TILTLEDISVSFDGFRALNNLNLYIGVGELRCIIGPNGAGKTTLMDVITGKTRPSHGKAW 107 Query: 63 ELDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKA 122 + + + ++A+AGI R FQ +F ++V EN+ + +T ++V+ A R + Sbjct: 108 FGETLDLTQMSEVQIAQAGIGRKFQKPTVFEALSVFENLELA--QKTDKSVW-ASLRARL 164 Query: 123 AREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAA 182 + E+ +++ ++LD + + R A LS+G ++ LEI L DPQLL LDEP A Sbjct: 165 SGEQ----KDRIAQVLDTIRLTSSVNRPAGLLSHGQKQFLEIGMLLMQDPQLLLLDEPVA 220 Query: 183 GMNATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQK 242 GM E EL K A +++++EHD+ + + + +TVL G +AEG VQ Sbjct: 221 GMTDAETEFTAELF-KSLAGKHSLMVVEHDMGFVGSIADHVTVLHQGSVLAEGSLEQVQD 279 Query: 243 NPAVIEAYLG 252 N VIE YLG Sbjct: 280 NERVIEVYLG 289 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: 173 Number of extensions: 8 Number of successful extensions: 4 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: 290 Length adjustment: 25 Effective length of query: 230 Effective length of database: 265 Effective search space: 60950 Effective search space used: 60950 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: 47 (22.7 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