Align ABC transporter for Lactose, ATPase component (characterized)
to candidate 5207560 Shew_0094 ABC transporter-related protein (RefSeq)
Query= reanno::Smeli:SM_b20002 (358 letters) >FitnessBrowser__PV4:5207560 Length = 369 Score = 156 bits (394), Expect = 9e-43 Identities = 94/226 (41%), Positives = 135/226 (59%), Gaps = 12/226 (5%) Query: 20 KGVDLDI----KSGEFVVFVGPSGCGKSTLLRMIAGLEEISSGDLTI-DDVRMND----- 69 +G+ LD K+GE + VGPSG GKSTL+RMIAGL + SG++ D V + Sbjct: 16 EGIALDAEFVCKAGEVLAVVGPSGGGKSTLMRMIAGLTKPESGEIRYGDSVWFSSESGRY 75 Query: 70 VDPSKRGIAMVFQSYALYPHMTVRENMGFALRFAGVPRAEIEKRVNEAAHILELGALLDR 129 + P +R + V Q + L+P+MT N+ AL +P+AE R + + L L DR Sbjct: 76 LTPQQRHLGYVPQHFGLFPNMTALANVVAALDH--IPKAERVARAKDWLERVNLHGLPDR 133 Query: 130 KPKQLSGGQRQRVAIGRAIVRHPKIFLFDEPLSNLDAELRVHMRIEIARLHKQLATTIVY 189 P LSGGQRQRVA+ RA+ R P++ L DEP S +D E R + +E+ARL +QLA ++ Sbjct: 134 LPANLSGGQRQRVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKEQLAIPVIM 193 Query: 190 VTHDQVEAMTLADKIVVMRAGVVEQVGSPLDLYDDPANLFVAGFIG 235 VTHD EA+ LAD+++++ G + Q GSP ++ P N VA +G Sbjct: 194 VTHDLNEALLLADRMILISQGTLLQQGSPREVLSRPRNEAVAKQMG 239 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: 295 Number of extensions: 16 Number of successful extensions: 3 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: 369 Length adjustment: 29 Effective length of query: 329 Effective length of database: 340 Effective search space: 111860 Effective search space used: 111860 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