Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Pedo557:CA265_RS07485 Length = 252 Score = 135 bits (339), Expect = 1e-36 Identities = 83/205 (40%), Positives = 122/205 (59%), Gaps = 14/205 (6%) Query: 18 ALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIGGRDVTTV------E 71 AL ++LDI GEFV +GPSG GKSTL+ L L+ SSG + G +V+ + E Sbjct: 24 ALKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGTYVLNGTNVSHMSDDALAE 83 Query: 72 PADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQ---LEDYLD 128 ++++ VFQ++ L P T +N+ + G +K+R A AAR L+ L + +D Sbjct: 84 VRNQEIGFVFQTFNLLPRSTSLDNVALPLIYAGTS---KKDRDARAARALENVGLGNRMD 140 Query: 129 RKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQLGATMI 188 KP +LSGGQRQRVA+ RA++ NPS+ L DEP NLD K +++ LE +H + G T+I Sbjct: 141 HKPNELSGGQRQRVAVARALINNPSIILADEPTGNLDTKTSIEIMGLLEEIHSK-GNTII 199 Query: 189 YVTHDQVEAMTMADKIVVLNRGRIE 213 VTH++ + A +IV + G IE Sbjct: 200 LVTHEE-DIAQHAHRIVRMRDGLIE 223 Lambda K H 0.320 0.139 0.396 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: 190 Number of extensions: 5 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: 338 Length of database: 252 Length adjustment: 26 Effective length of query: 312 Effective length of database: 226 Effective search space: 70512 Effective search space used: 70512 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: 48 (23.1 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