Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__ANA3:7026050 Length = 376 Score = 150 bits (378), Expect = 7e-41 Identities = 117/360 (32%), Positives = 172/360 (47%), Gaps = 18/360 (5%) Query: 1 MQLALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVT 60 M + L +ISKK G L ++L +Q G + LLG + +GKT+L+RI+AGL+ +G++ Sbjct: 1 MSIRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIH 60 Query: 61 VDGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKN------IDARVREI 114 +DVT + VRDR V V+Q + + M VA N+A L++ +K I RV + Sbjct: 61 FGNRDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSKAEIQKRVSHL 120 Query: 115 ASRLHIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELT 174 + + RYP +LSGGQ+QR+ALARALA ++LLDEP LD K+R+ELR L Sbjct: 121 LEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLR 180 Query: 175 QLFAAGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDP 234 L + T V+ T + EAL L V+ G + Q E++ PNS R D Sbjct: 181 SLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNS----RFVFDF 236 Query: 235 PMNLMAASATAQGVRLQGGAELTLPLPQGAATAAGLTVGVRASALRVHARPGDVS--VAG 292 N+ A+ Q R G +P P+ + VR+ L + +P + Sbjct: 237 LGNVNRFEASWQQNRWTNGDAFLVP-PEQTPLQQNGALYVRSHELALADKPNSQAHIPFT 295 Query: 293 VVELAEISGSDTFVHASTPWGD---LVAQLTGVHYFELG--TAITLHLDPAQAYVFGADG 347 +V + + A W A T H ELG ++ P AY FG G Sbjct: 296 IVAITPVGAEVRVELAPIGWQSEELWEATFTHHHLQELGLQKGSLVYATPRTAYFFGEQG 355 Lambda K H 0.318 0.133 0.375 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: 258 Number of extensions: 9 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: 363 Length of database: 376 Length adjustment: 30 Effective length of query: 333 Effective length of database: 346 Effective search space: 115218 Effective search space used: 115218 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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