Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate PfGW456L13_1569 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1569 Length = 372 Score = 243 bits (619), Expect = 8e-69 Identities = 141/304 (46%), Positives = 193/304 (63%), Gaps = 25/304 (8%) Query: 4 VRLVDVWKVFGEV----TAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQ 59 V + V KV+G+ A++ + L+++D EF LLGPSGCGKTT LRMIAG E P+ G+ Sbjct: 12 VSIRSVRKVYGDPKTGPVALKSIDLDIRDNEFFTLLGPSGCGKTTLLRMIAGFEFPTEGE 71 Query: 60 IYIGDKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKL----RKVPRQE 115 I + + +AD PP R + VFQ YAL+PHMT+ +N+AF L+ + + + + Sbjct: 72 ILLYGENIADR------PPFQRPVNTVFQHYALFPHMTIAENLAFGLESHPMGKVLHKTQ 125 Query: 116 IDQRVREVAELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLR 175 + +RVRE+ L+ + NRKP +LSGGQ+QRVAL RA+ P+V L+DEPLS LD KLR Sbjct: 126 LAERVREMLALVQMERFANRKPAQLSGGQQQRVALARALAPHPKVLLLDEPLSALDLKLR 185 Query: 176 VRMRAELKKLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTF 235 MR ELK +Q + G+T I+VTHDQ EA+TM DRIAV++ G +QQVG P+++Y++P N F Sbjct: 186 QAMREELKTIQARTGITFIFVTHDQEEALTMSDRIAVLSEGEVQQVGRPEDIYERPRNRF 245 Query: 236 VAGFIGSPPMNFLDAIVT--EDGFVDFGEFRLKLLPDQ--FEVLGELGYVGREVIFGIRP 291 VA FIG NF++ VT EDG F LP Q +V VG V +RP Sbjct: 246 VADFIGE--TNFIEGTVTRVEDGLAWFAGPAGHPLPAQPCSDV-----RVGANVTLSVRP 298 Query: 292 EDLY 295 E L+ Sbjct: 299 ERLH 302 Lambda K H 0.323 0.142 0.406 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: 362 Number of extensions: 15 Number of successful extensions: 3 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: 372 Length of database: 372 Length adjustment: 30 Effective length of query: 342 Effective length of database: 342 Effective search space: 116964 Effective search space used: 116964 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 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