Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_011319366.1 AVA_RS13165 ABC transporter ATP-binding protein
Query= uniprot:D8J1T6 (255 letters) >NCBI__GCF_000204075.1:WP_011319366.1 Length = 491 Score = 139 bits (350), Expect = 1e-37 Identities = 79/235 (33%), Positives = 131/235 (55%), Gaps = 14/235 (5%) Query: 6 LKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFELD 65 L++ ++SKRF A + + ++++ G+I+G++G NGAGKTT N+I GLYQPD G L Sbjct: 3 LRLENISKRFNSFIANDNISLSVDAGKIHGILGENGAGKTTLMNIIGGLYQPDAGEIYLQ 62 Query: 66 GKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAARE 125 +P ++P++ K GI +Q+ L ++TV EN+++G ++N + R K ++ Sbjct: 63 DQPVKITSPNQAIKLGIGMIYQHFMLVPQLTVTENIILG-----RENSWRLNLRQK--QQ 115 Query: 126 EEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGMN 185 E AA+ + G+ L G Q+R+EI + L +LL LDEP A + Sbjct: 116 EIAALSQA-------YGLEIDPTAKVEDLPVGTQQRVEILKVLYRQAKLLILDEPTAVLT 168 Query: 186 ATEKLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADV 240 TE L +L ++ A G TI+ I H ++ ++ LC+ +TVL GK +A D+ Sbjct: 169 PTEVESLINILRQLAAAGNTIIFISHKLEEVINLCDTVTVLRRGKVVATTTTKDM 223 Score = 56.6 bits (135), Expect = 9e-13 Identities = 55/225 (24%), Positives = 96/225 (42%), Gaps = 29/225 (12%) Query: 17 GLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFELDGKPYSPSA--- 73 G+ A++ V + G+I G+ G +G G+ + I L GT +L+ SP Sbjct: 265 GILAVHNVSFQLLAGEILGIAGVDGNGQRELADAIANLRGILNGTIQLNSS--SPQQKIG 322 Query: 74 --PHEVAKAGIARTF---QNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAREEEA 128 P + K G+ F QN+ L V + + H K +V + H +E Sbjct: 323 YIPEDRQKMGLVLQFTIAQNLIL----NVFKKIPFCRHFLLKSSV---IKHHAQVAMQEF 375 Query: 129 AIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGMNATE 188 IR + + LS G+Q+++ +AR LA P L+ +P G++ Sbjct: 376 DIRATGEDI------------QVSQLSGGNQQKVVLARELAGKPDLIVAMQPTRGLDVGA 423 Query: 189 KLGLRELLVKIQAEGKTILLIEHDVKLMMGLCNRITVLDYGKPIA 233 + L+ + G IL I +++ +M + +RI V+ GK +A Sbjct: 424 TSAVHSRLLTERDRGAAILYISTELEEVMAMSDRIAVIYRGKFVA 468 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: 269 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 255 Length of database: 491 Length adjustment: 29 Effective length of query: 226 Effective length of database: 462 Effective search space: 104412 Effective search space used: 104412 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: 49 (23.5 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