Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AZOBR_RS28565 AZOBR_RS28565 sugar ABC transporter ATPase
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__azobra:AZOBR_RS28565 Length = 602 Score = 219 bits (559), Expect = 8e-62 Identities = 120/254 (47%), Positives = 162/254 (63%), Gaps = 12/254 (4%) Query: 3 EKSNEVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPD 62 E S +L+V +SK FGG+ VG+ + +++ LIGPNGAGK+T N++TG+ + D Sbjct: 342 EPSAGPLLEVTDVSKAFGGVVTADKVGLRLHAHRIHALIGPNGAGKSTLINILTGVISAD 401 Query: 63 AGTFELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVF 122 +GT LAG+ H A GIARTFQN+RLF MT L+NV++G H R G Sbjct: 402 SGTIRLAGQDITRGTAHARAARGIARTFQNLRLFGSMTVLDNVLIGAHARIGVT------ 455 Query: 123 RTKGFKAEEAAIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALD 182 EE A+AK A+ +LD+VG+G+ A A +L YG QRR+E+ARALA DP L+ LD Sbjct: 456 -----GREEDAVAK-AKAVLDFVGLGEHAGALAGSLPYGLQRRVELARALAGDPVLLLLD 509 Query: 183 EPAAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPA 242 EPAAG+N E +L +LI RI +L++EHD+ LVM + D + VLD G IAEG P Sbjct: 510 EPAAGLNPRETAELGQLIKRIGQLGVAVLMVEHDMGLVMRISDEIVVLDRGVVIAEGAPR 569 Query: 243 EVQKNEKVIEAYLG 256 ++Q N +VIEAYLG Sbjct: 570 DIQTNPRVIEAYLG 583 Lambda K H 0.319 0.137 0.384 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: 424 Number of extensions: 18 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: 260 Length of database: 602 Length adjustment: 31 Effective length of query: 229 Effective length of database: 571 Effective search space: 130759 Effective search space used: 130759 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 (21.7 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