Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate 6938538 Sama_2641 polyamine ABC transporter, ATP-binding protein (RefSeq)
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__SB2B:6938538 Length = 378 Score = 226 bits (575), Expect = 1e-63 Identities = 124/325 (38%), Positives = 193/325 (59%), Gaps = 9/325 (2%) Query: 9 ICKSYDGTPITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGDLLIDNQRVN 68 + K +D + L I GE +G SG GKSTLLR++AG E T G + +D Q + Sbjct: 26 VSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTEGRIYLDGQDIT 85 Query: 69 DLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAEILQLDKLLE 128 DLPP +R + M+FQSYAL+PHMTV +N+AFGLK + K +I +RV+ + +++ +++ + Sbjct: 86 DLPPYERPINMMFQSYALFPHMTVEQNIAFGLKQDKMSKADISQRVQEMLKLVHMEQYAK 145 Query: 129 RKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARLHQRIRSTMI 188 RKP LSGGQRQRVA+ R++ + PK+ L DEP+ LD LR QM++E+ + +R+ T + Sbjct: 146 RKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERVGVTCV 205 Query: 189 YVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQMNFVEVRAIS 248 VTHDQ EAMT+A +I +++ G IAQVG P+ +Y P +R +A F+G+ +N + I Sbjct: 206 MVTHDQEEAMTMAGRIAIMSDGWIAQVGSPMDIYESPNSRMIAEFIGT--VNLFDCEIIE 263 Query: 249 ASPETVTIELPSGYPLTLPVDGSAVSPGDP-LTLGIRPEHFVM---PDEADFTF-HGQIT 303 + ++ P+ L G S D + L +RPE ++ E ++ + G++ Sbjct: 264 DEADHAILKSPTLPQPFLIGHGVTTSLEDKHVWLAVRPEKTLITREQPEGEYNWARGKVH 323 Query: 304 VAERLGQYNLLYLTLERLQDVITLC 328 LG ++ Y+ LE D I C Sbjct: 324 DIAYLGGLSVYYIKLE--DDKIIQC 346 Lambda K H 0.322 0.139 0.405 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: 308 Number of extensions: 12 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: 371 Length of database: 378 Length adjustment: 30 Effective length of query: 341 Effective length of database: 348 Effective search space: 118668 Effective search space used: 118668 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 (21.9 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