Align ABC transporter for D-sorbitol, ATPase component (characterized)
to candidate 202699 SO3602 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)
Query= reanno::pseudo6_N2E2:Pf6N2E2_1960 (365 letters) >FitnessBrowser__MR1:202699 Length = 376 Score = 211 bits (537), Expect = 3e-59 Identities = 113/315 (35%), Positives = 188/315 (59%), Gaps = 19/315 (6%) Query: 3 TLKIENLKKGFEGLSIIKGIDLEVKDKEFVVFVGPSGCGKSTLLRLIAGLEDVTSGTIEL 62 ++++ N+ K F + ++L++++ E + +GPSG GK+TLLR+IAGLE SG I Sbjct: 2 SIRLTNISKKFGQFQALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGHIHF 61 Query: 63 DGRDITEVTPAKRDLAMVFQTYALYPHMTVRKNLSFALDLAGEKK----PDVERKVAEAA 118 RD+T+V R + VFQ YAL+ HMTV N++F L++ +K+ +++++V+ Sbjct: 62 GNRDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSAAEIQKRVSHLL 121 Query: 119 RILELGSLLDRKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQTRLELSR 178 +++LG L R P+QLSGGQ+QR+A+ RA+ P++ L DEP LDA +R + R L Sbjct: 122 EMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLRS 181 Query: 179 LHKELQATMIYVTHDQVEAMTLATKVVVLNAGRIEQIGSPLELYHHPANLFVAGFLGTPK 238 LH EL+ T ++VTHDQ EA+ L+ +VVV++ G IEQ+ +P+ELY P + FV FLG Sbjct: 182 LHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLG--- 238 Query: 239 MGFLQATVHAVHASGVEVRFASGTTLLIPRDSSALSVGQSVTIGIRPEHLTL----SAEG 294 V+ A+ + R+ +G ++P + + L Q+ + +R L L +++ Sbjct: 239 ------NVNRFEANWQQNRWTNGDAFIVPPEQTPLQ--QNGALYVRSHELALADKPNSQA 290 Query: 295 QVPVTTDVTERLGSD 309 +P T +G++ Sbjct: 291 HIPFTIVAITPIGAE 305 Lambda K H 0.319 0.135 0.380 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: 297 Number of extensions: 7 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: 365 Length of database: 376 Length adjustment: 30 Effective length of query: 335 Effective length of database: 346 Effective search space: 115910 Effective search space used: 115910 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