Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate Ac3H11_4180 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4180 Length = 367 Score = 249 bits (635), Expect = 1e-70 Identities = 142/315 (45%), Positives = 192/315 (60%), Gaps = 19/315 (6%) Query: 4 VRLVDVWKVF-GEVTAVREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYI 62 VR V K + GE VR + L+++ GEF+ LLGPSG GKTTTL M+AG E P+ G I + Sbjct: 9 VRFTGVQKTYDGEQLVVRALDLDIQRGEFLSLLGPSGSGKTTTLMMLAGFESPTAGDILL 68 Query: 63 GDKLVADPEKGIFVPPKDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVRE 122 K + PP R+ MVFQ+YAL+PH+TV +N+A+PL +RKVP+ E +RV++ Sbjct: 69 DGKQITR------TPPHKRNFGMVFQNYALFPHLTVGENVAYPLTVRKVPKAEQAERVKK 122 Query: 123 VAELLGLTELLNRKPRELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAEL 182 +++ LT + +R P LSGGQ+QRVAL RA+V PQ+ LMDEPL LD +LR M+ EL Sbjct: 123 ALDMVRLTGMADRLPARLSGGQQQRVALARALVFNPQLVLMDEPLGALDKQLREHMQIEL 182 Query: 183 KKLQRQLGVTTIYVTHDQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGS 242 K+L RQLGVT +YVTHDQ EA+TM DR+AV N GV+QQ+ + +Y+ P+N FVAGF+G Sbjct: 183 KELHRQLGVTFVYVTHDQGEALTMSDRVAVFNEGVIQQLADVESLYETPSNRFVAGFVG- 241 Query: 243 PPMNFLDAIVTEDGFVDFGEFRLKLLPDQFEVLG---ELGYVGREVIFGIRPEDLYDAMF 299 D+ V G +P F + G VG V +RPE + + Sbjct: 242 ------DSTVLSGTLQGAGADAAIQMPGGFLLPGVNVNQAPVGARVQACVRPERV--VLL 293 Query: 300 AQVRVPGENLVRAVV 314 Q P N + A V Sbjct: 294 PQSEYPRPNAIPATV 308 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: 363 Number of extensions: 17 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: 372 Length of database: 367 Length adjustment: 30 Effective length of query: 342 Effective length of database: 337 Effective search space: 115254 Effective search space used: 115254 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