Align ABC transporter for D-Maltose and D-Trehalose, ATPase component (characterized)
to candidate AZOBR_RS30410 AZOBR_RS30410 ABC transporter ATP-binding protein
Query= reanno::Smeli:SMc03065 (362 letters) >FitnessBrowser__azobra:AZOBR_RS30410 Length = 371 Score = 247 bits (631), Expect = 3e-70 Identities = 138/290 (47%), Positives = 180/290 (62%), Gaps = 6/290 (2%) Query: 3 GLLLKDIRKSYGAVDVIHGIDLDIKEGEFVVFVGPSGCGKSTLLRMIAGLEEITGGDMFI 62 G+ + + SYG+ V+ I LDIK GEF F+GPSGCGK+TLLR+IAG G + I Sbjct: 18 GVRIDGVDLSYGSHRVLKDIHLDIKPGEFFAFLGPSGCGKTTLLRLIAGFNTAQRGAVTI 77 Query: 63 DGERVNDVPPSKRGIAMVFQSYALYPHMTVYDNMAFGMRIARESKEEIDRRVRGAADMLQ 122 G ++ +P KR + MVFQSYAL+PHMTV N+AFG+ R + EI+RRV A D++ Sbjct: 78 GGRDISGLPAHKRDVGMVFQSYALWPHMTVRRNVAFGLEERRVPRAEIERRVDAALDLVG 137 Query: 123 LTPYLDRLPKALSGGQRQRVAIGRAICRNPKVFLFDEPLSNLDAALRVATRIEIAKLSER 182 L DR P LSGGQ+QRVA+ R I PKV L DEPLSNLDA LRV R E+ L + Sbjct: 138 LKHLADRRPSQLSGGQQQRVALARTIVIEPKVLLLDEPLSNLDAKLRVQMRQELLSLQRK 197 Query: 183 MSDTTMIYVTHDQVEAMTLADRIVVLSAGHIEQVGAPLELYERPANLFVARFIGSPAMNV 242 + TT I+VTHDQ EA T+ DRI V+ G ++QVG P ELY+ PANLFVA F+G+ NV Sbjct: 198 LGLTT-IFVTHDQEEANTICDRIAVMEDGIVQQVGTPQELYDHPANLFVAGFLGT--ANV 254 Query: 243 IPATITATGQQTAVSLAGGKSVTLDVPTNASENGKTASFGVRPEDLRVTE 292 + + A TA + GG + L + E G RP++L + + Sbjct: 255 LEGQVRAVDGGTAFVMGGGVPIPL---PHGVEPGAAGKLMFRPQNLFIRQ 301 Lambda K H 0.320 0.137 0.387 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: 365 Number of extensions: 13 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 362 Length of database: 371 Length adjustment: 30 Effective length of query: 332 Effective length of database: 341 Effective search space: 113212 Effective search space used: 113212 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