Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate RR42_RS13785 RR42_RS13785 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >FitnessBrowser__Cup4G11:RR42_RS13785 Length = 368 Score = 488 bits (1257), Expect = e-143 Identities = 252/368 (68%), Positives = 287/368 (77%), Gaps = 10/368 (2%) Query: 1 MARISLDLAHSYKPNPQQDSDYALLPLKMEFEDGGAYALLGPSGCGKTTMLNIMSGLLVP 60 M RI LDL+HSY+P+PQ D DYALLPLK F DGGAYALLGPSGCGKTT+LN +SGL P Sbjct: 1 MTRIDLDLSHSYRPDPQADEDYALLPLKFTFNDGGAYALLGPSGCGKTTLLNCISGLQRP 60 Query: 61 SHGKVLFDGRDVTRASPQERNIAQVFQFPVIYDTMTVAENLAFPLRNRKVPEGQIKQRVG 120 SHG V FDGRDVT A+PQ RNIAQVFQFPVIYDTMTV ENLAFPLRNR VP Q+K+RVG Sbjct: 61 SHGTVSFDGRDVTAATPQARNIAQVFQFPVIYDTMTVGENLAFPLRNRGVPAAQVKERVG 120 Query: 121 VIAEMLEMSGQLNQRAAGLAADAKQKISLGRGLVRADVAAVLFDEPLTVIDPHLKWQLRR 180 +AEML++S L++RA+GLAADAKQKISLGRGLVR DV+A+LFDEPLTVIDPHLKWQLRR Sbjct: 121 RVAEMLDLSASLDRRASGLAADAKQKISLGRGLVRQDVSAILFDEPLTVIDPHLKWQLRR 180 Query: 181 KLKQIHHELKLTLIYVTHDQVEALTFADQVVVMTRGKAVQVGSADALFERPAHTFVGHFI 240 KLK+IHHE +LTLIYVTHDQ EALTFADQVVVM+RG+AVQVG ADALFERPAHTFVG+FI Sbjct: 181 KLKEIHHEFRLTLIYVTHDQTEALTFADQVVVMSRGRAVQVGPADALFERPAHTFVGNFI 240 Query: 241 GSPGMNFLPAHRDGENLSVAGHR----LASPVGRAL-PAGALQVGIRPEYLALAQPQQAG 295 GSPGMNFL + +AG R A V AL AG+ +VG+RPEYL LA Sbjct: 241 GSPGMNFLTGAWHDGAIEIAGRRYMPEFAPTVAAALQAAGSFKVGVRPEYLRLAASTDPQ 300 Query: 296 ALPGTVVQVQDIGTYQMLTAKVGE-----HTVKARFTPETRLPSSGDTAWLQVLGEHTCY 350 A+P V + QDIGTY ++TA V + TV+ R E +G+TAWL V HTCY Sbjct: 301 AVPARVERAQDIGTYWLITATVRDASGHAATVRGRLGNEGAALRAGETAWLSVFNRHTCY 360 Query: 351 YKNEELLA 358 Y NEEL+A Sbjct: 361 YVNEELVA 368 Lambda K H 0.320 0.136 0.395 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: 444 Number of extensions: 13 Number of successful extensions: 3 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: 358 Length of database: 368 Length adjustment: 29 Effective length of query: 329 Effective length of database: 339 Effective search space: 111531 Effective search space used: 111531 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 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