Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 5207560 Shew_0094 ABC transporter-related protein (RefSeq)
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__PV4:5207560 Length = 369 Score = 146 bits (368), Expect = 1e-39 Identities = 87/228 (38%), Positives = 129/228 (56%), Gaps = 8/228 (3%) Query: 16 QTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGD------RRV 69 Q E D + E VGPSG GK+T +RMIAGL G + GD Sbjct: 14 QQEGIALDAEFVCKAGEVLAVVGPSGGGKSTLMRMIAGLTKPESGEIRYGDSVWFSSESG 73 Query: 70 NDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAAKILDIAHLL 129 + P+ R + V Q++ L+P+MT N+ L +PKAE R ++ + +++ L Sbjct: 74 RYLTPQQRHLGYVPQHFGLFPNMTALANVVAALD--HIPKAERVARAKDWLERVNLHGLP 131 Query: 130 DRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTV 189 DR P LSGGQRQRVAL RA+ REP+V L+DEP S +D + R ++ E+ +L ++L V Sbjct: 132 DRLPANLSGGQRQRVALARALAREPRVLLLDEPFSAVDRETRERLYLELARLKEQLAIPV 191 Query: 190 IYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIG 237 I VTHD EA+ + DR++++ G + Q +P+ V S+P+N VA +G Sbjct: 192 IMVTHDLNEALLLADRMILISQGTLLQQGSPREVLSRPRNEAVAKQMG 239 Lambda K H 0.321 0.138 0.395 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: 301 Number of extensions: 15 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: 384 Length of database: 369 Length adjustment: 30 Effective length of query: 354 Effective length of database: 339 Effective search space: 120006 Effective search space used: 120006 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: 50 (23.9 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