Align Maltose-transporting ATPase (EC 3.6.3.19) (characterized)
to candidate PfGW456L13_1569 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::psRCH2:GFF857 (371 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1569 Length = 372 Score = 242 bits (618), Expect = 1e-68 Identities = 150/360 (41%), Positives = 205/360 (56%), Gaps = 19/360 (5%) Query: 3 SVTLRDICKSYDGTPIT-----RHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITS 57 +V++R + K Y G P T + IDLDI D EF +GPSGCGK+TLLR+IAG E T Sbjct: 11 AVSIRSVRKVY-GDPKTGPVALKSIDLDIRDNEFFTLLGPSGCGKTTLLRMIAGFEFPTE 69 Query: 58 GDLLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDK----REIKRR 113 G++L+ + + D PP R V VFQ YAL+PHMT+AEN+AFGL+ + K ++ R Sbjct: 70 GEILLYGENIADRPPFQRPVNTVFQHYALFPHMTIAENLAFGLESHPMGKVLHKTQLAER 129 Query: 114 VEAVAEILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMR 173 V + ++Q+++ RKP LSGGQ+QRVA+ R + PKV L DEPLS LD LR MR Sbjct: 130 VREMLALVQMERFANRKPAQLSGGQQQRVALARALAPHPKVLLLDEPLSALDLKLRQAMR 189 Query: 174 IEIARLHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGF 233 E+ + R T I+VTHDQ EA+T++D+I VL+ GE+ QVG+P +Y P+NRFVA F Sbjct: 190 EELKTIQARTGITFIFVTHDQEEALTMSDRIAVLSEGEVQQVGRPEDIYERPRNRFVADF 249 Query: 234 LGSPQMNFVEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGDPLTLGIRPEHF-VMPD 292 +G + NF+E P+G+PL S V G +TL +RPE ++P Sbjct: 250 IG--ETNFIEGTVTRVEDGLAWFAGPAGHPLPAQ-PCSDVRVGANVTLSVRPERLHLVPA 306 Query: 293 EADFTFHGQITVAERLG---QYNLLYLTLERLQDVITLCVDGNLRVTEGETFAAGLKADK 349 + +I LG QY + RL CVD + R G AGL D+ Sbjct: 307 TTENALPCRIEAQIYLGTDLQYQVSLSDGSRLTVRTPNCVDQSKRFAVGS--QAGLLFDQ 364 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: 360 Number of extensions: 20 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: 371 Length of database: 372 Length adjustment: 30 Effective length of query: 341 Effective length of database: 342 Effective search space: 116622 Effective search space used: 116622 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: 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