Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Ac3H11_2058 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2058 Length = 360 Score = 244 bits (623), Expect = 3e-69 Identities = 126/274 (45%), Positives = 178/274 (64%), Gaps = 8/274 (2%) Query: 21 VKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIA 80 VK + E+ G ++GPSGCGK+TTLRM+AGLE+ T G IFIG KDVT + P R+++ Sbjct: 27 VKGISFEVPRGTLTTILGPSGCGKTTTLRMIAGLESPTSGEIFIGGKDVTTLGPAQRNVS 86 Query: 81 MVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQ 140 M+FQ+YAL+PHM V EN+ + L+++G+ +++ + EA +GL F +R P LSGGQ Sbjct: 87 MMFQSYALFPHMNVVENVMYGLRMSGQPKEQARAKAVEALRGVGLVGFDDRLPSELSGGQ 146 Query: 141 RQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEAL 200 +QRVA+ RA+V P+V L DEPLSNLDA+LR + R +I ALQ++L +T YVTHDQ EA+ Sbjct: 147 QQRVALARALVLEPEVLLFDEPLSNLDARLRREMREEIRALQQRLSLTVAYVTHDQAEAM 206 Query: 201 TMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARI 260 + D+I V+ G + Q G+PR LY+ P + FVAGF+G + +V D D T + Sbjct: 207 AVSDQIIVMNQGLIAQKGSPRALYETPHSEFVAGFMGEAML---FPAVADADGT-----V 258 Query: 261 KLSPETLAAMTPEDNGRITIGFRPEALEIIPEGE 294 L P L +G + + RPEA I +GE Sbjct: 259 ALGPLVLRPRVAVKSGPVKVAVRPEAWRITRQGE 292 Lambda K H 0.316 0.135 0.380 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: 377 Number of extensions: 19 Number of successful extensions: 2 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: 376 Length of database: 360 Length adjustment: 30 Effective length of query: 346 Effective length of database: 330 Effective search space: 114180 Effective search space used: 114180 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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