Align ABC transporter for D-Mannitol, D-Mannose, and D-Sorbitol, ATPase component (characterized)
to candidate PfGW456L13_2830 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::WCS417:GFF2490 (367 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2830 Length = 361 Score = 244 bits (623), Expect = 3e-69 Identities = 125/296 (42%), Positives = 193/296 (65%), Gaps = 8/296 (2%) Query: 4 LKIKNLQKGFEG----FSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGT 59 ++++N+ K + + + +++ D EF +GPSGCGK+TLLR IAG E VS+G Sbjct: 7 IEVRNVSKRYSDDPGLAPALDNVSVDIADNEFFTLLGPSGCGKTTLLRTIAGFEHVSDGE 66 Query: 60 IELDGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAAR 119 I L G + ++ P KR + VFQ+YAL+PHMSV +N++F L++ G+D+KL+ +V E Sbjct: 67 IRLAGEPVNDLPPFKRRVNTVFQSYALFPHMSVAQNIAFGLEMQGLDRKLIPQRVDEMLA 126 Query: 120 ILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARL 179 ++++ L +RKP +LSGGQ+QRVA+ RA+ PK+ L DEPLS LD LR +M++EL R+ Sbjct: 127 LVQMQHLAKRKPAELSGGQQQRVALARALAPKPKVLLLDEPLSALDLKLRKEMQVELKRV 186 Query: 180 HKELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKM 239 KE T I+VTHDQ EA+TL+D++ V+++G+I Q+GSP E+Y +P + FVA F+G + Sbjct: 187 QKEAGITFIFVTHDQEEALTLSDRIAVMSAGKILQIGSPNEIYERPQHQFVAQFIG--DI 244 Query: 240 GFLKGKVTRVESQSCEVQLDAGTLINLPLSGATLSVGSAVTLGIRPEHLEIASPGQ 295 FL G + R + Q+ ++ + G + +P GS V L RPE ++ P Q Sbjct: 245 NFLPGHIKRGQ-QNEKLFVPNGMPVEIPCPAQGFD-GSKVQLAFRPERSQLVEPTQ 298 Lambda K H 0.319 0.136 0.384 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: 323 Number of extensions: 9 Number of successful extensions: 1 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: 367 Length of database: 361 Length adjustment: 29 Effective length of query: 338 Effective length of database: 332 Effective search space: 112216 Effective search space used: 112216 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