Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate Ac3H11_2058 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::Phaeo:GFF1302 (334 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2058 Length = 360 Score = 233 bits (593), Expect = 7e-66 Identities = 136/336 (40%), Positives = 193/336 (57%), Gaps = 31/336 (9%) Query: 4 IKLESVTKNFGPVE----VIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGT 59 I ++TK +G + + + G T +GPSGCGK+T LR+IAGLE TSG Sbjct: 8 IVFRNITKRYGTDSSAALAVKGISFEVPRGTLTTILGPSGCGKTTTLRMIAGLESPTSGE 67 Query: 60 IRIDGEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAA 119 I I G+D T + PA+R ++M+FQSYAL+PHM+V +N+ + ++M+G P ++ + + A Sbjct: 68 IFIGGKDVTTLGPAQRNVSMMFQSYALFPHMNVVENVMYGLRMSGQPKEQARAKAVEALR 127 Query: 120 ALNLTDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISEL 179 + L + DR P +LSGGQ+QRVA+ RA+V EP LFDEPLSNLDA LR MR EI L Sbjct: 128 GVGLVGFDDRLPSELSGGQQQRVALARALVLEPEVLLFDEPLSNLDARLRREMREEIRAL 187 Query: 180 HKRLATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKM 239 +RL+ T+ YVTHDQ EAM ++D+I+V+ G+I Q GSP LY P + FVAGF+G + Sbjct: 188 QQRLSLTVAYVTHDQAEAMAVSDQIIVMNQGLIAQKGSPRALYETPHSEFVAGFMGEAML 247 Query: 240 ---------NLLTGP------QAAQHNAATIGIRPEHLSIS-ETEGMWAGTIGVSEHLGS 283 + GP A + + +RPE I+ + EG+ + S +LG+ Sbjct: 248 FPAVADADGTVALGPLVLRPRVAVKSGPVKVAVRPEAWRITRQGEGLLPARLAKSAYLGA 307 Query: 284 ----------DTFFHVQCDAFDDPLTVRASGELDLG 309 + F V D DD L V +L LG Sbjct: 308 VHEYTFETALGSIFVVSSD-LDDVLAVGDDVQLGLG 342 Lambda K H 0.320 0.138 0.400 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: 310 Number of extensions: 10 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: 334 Length of database: 360 Length adjustment: 29 Effective length of query: 305 Effective length of database: 331 Effective search space: 100955 Effective search space used: 100955 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