Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate H281DRAFT_02629 H281DRAFT_02629 carbohydrate ABC transporter ATP-binding protein, CUT1 family (TC 3.A.1.1.-)
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__Burk376:H281DRAFT_02629 Length = 381 Score = 373 bits (957), Expect = e-108 Identities = 204/371 (54%), Positives = 261/371 (70%), Gaps = 13/371 (3%) Query: 1 MASVTLRDICKSYDGT-PITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSGD 59 MA+++LR I K++DG P+ R ++L+I + EF VF+GPSGCGKSTLLR++AGLED T GD Sbjct: 1 MAAISLRGIQKTFDGNAPVLRDLNLEIGEHEFCVFLGPSGCGKSTLLRIVAGLEDQTDGD 60 Query: 60 LLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVAE 119 + I + +N +P +R V MVFQSYAL+PHMTV ENMAFGLKLA K EI R+V A Sbjct: 61 VSIGGRTMNSVPAAERGVAMVFQSYALFPHMTVYENMAFGLKLARTPKAEIDRKVREAAH 120 Query: 120 ILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIARL 179 +LQLD LL RKP++LSGGQRQRVAIGR +VREP VFLFDEPLSNLDA LR Q RIEIARL Sbjct: 121 VLQLDALLARKPRELSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDAALRGQTRIEIARL 180 Query: 180 HQR-IRSTMIYVTHDQVEAMTLADKIVVLNA-------GEIAQVGQPLHLYHYPKNRFVA 231 HQR +++++YVTHDQ+EAMTLADKIV+L+A G IAQ+G PL LYH P+++FVA Sbjct: 181 HQRYAQASVVYVTHDQIEAMTLADKIVLLHAGAETQRLGSIAQIGAPLELYHRPRSKFVA 240 Query: 232 GFLGSPQMNFVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHFVMP 291 GF+GSP+MNF++ + ++V + +P G L + VDG + PG +TLGIRPEH V Sbjct: 241 GFIGSPRMNFIDGVVERIADDSVEVSMP-GTALRVLVDGRRLKPGQRVTLGIRPEH-VRF 298 Query: 292 DEADFTFHGQITVAERLGQYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADKCH 351 D T + E+LG+++ YL + + G+L V GE A L AD CH Sbjct: 299 DGGTQTLAVNALLTEQLGEHS--YLHADHAGGTLIAKAPGDLHVRNGERLALHLPADACH 356 Query: 352 LFRENGEACTR 362 LF E+G A R Sbjct: 357 LFDEDGIALHR 367 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: 420 Number of extensions: 16 Number of successful extensions: 5 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: 381 Length adjustment: 30 Effective length of query: 341 Effective length of database: 351 Effective search space: 119691 Effective search space used: 119691 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