Align ABC transporter for Lactose, ATPase component (characterized)
to candidate GFF729 PGA1_c07440 ABC transporter, ATP binding protein
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__Phaeo:GFF729 Length = 353 Score = 369 bits (948), Expect = e-107 Identities = 197/352 (55%), Positives = 249/352 (70%), Gaps = 7/352 (1%) Query: 1 MSELQLSDVRKSYGGLEVIKGVDLDIKSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDL 60 M+ + L+ K YG ++VI VDL I GEF VFVGPSGCGKSTLLRMIAGLEE SSG++ Sbjct: 1 MTGVTLAKAVKKYGDVQVIHDVDLSIDDGEFCVFVGPSGCGKSTLLRMIAGLEETSSGNI 60 Query: 61 TIDDVRMNDVDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHI 120 I D + +D + RG+AMVFQSYALYPHMTV +NMGF L+ G P+ +I ++V EA+ I Sbjct: 61 HIGDRDVTRLDAADRGVAMVFQSYALYPHMTVEDNMGFGLKMNGHPKEKIREKVAEASRI 120 Query: 121 LELGALLDRKPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLH 180 L+L L RKPK LSGGQRQRVAIGRAIVR P++FLFDEPLSNLDAELRV MR+EIARLH Sbjct: 121 LKLDDYLKRKPKALSGGQRQRVAIGRAIVRGPEVFLFDEPLSNLDAELRVDMRVEIARLH 180 Query: 181 KQLATTIVYVTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIGSPKMN 240 K++ T++YVTHDQVEAMTLADKIVV+RAG VEQVGSP++LY +P N FVAGFIGSP MN Sbjct: 181 KEIGATMIYVTHDQVEAMTLADKIVVLRAGRVEQVGSPMELYANPDNRFVAGFIGSPSMN 240 Query: 241 FLKGVIEIDEDQAYARLPDYGDAKIPVTLQAAA-GTAVTIGIRPEHFDEAGPAALDLAID 299 FL+G ++ D +P + ++ ++ A G+ V +G+RP+H A L +D Sbjct: 241 FLEGTVQGDG----VVVPALENRRVATSVALPADGSKVLLGLRPQHLSVTA-ADSSLVLD 295 Query: 300 MLEHLGGETFAYARHHGNGELIVVETKNGRGLKTGDRLTARFDPVSVLVFDG 351 + E LGG ++ Y GE ++VET+ L G + FD +FDG Sbjct: 296 LRERLGGVSYDYL-STPTGEKLIVETRGDEALPEGTAVALGFDDADAYIFDG 346 Lambda K H 0.321 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: 403 Number of extensions: 17 Number of successful extensions: 4 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: 358 Length of database: 353 Length adjustment: 29 Effective length of query: 329 Effective length of database: 324 Effective search space: 106596 Effective search space used: 106596 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