Align MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized)
to candidate Ac3H11_1610 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1610 Length = 362 Score = 220 bits (560), Expect = 5e-62 Identities = 130/359 (36%), Positives = 200/359 (55%), Gaps = 28/359 (7%) Query: 4 LNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELK 63 L L + K Y S +V+ +L ++ EF+ +GPSGCGK+TTL+MVAG E +T G ++ Sbjct: 4 LQLTDVTKFY--GSTCAVQSMNLSVEKGEFVSLLGPSGCGKTTTLQMVAGFEAVTSGRIE 61 Query: 64 IDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQIL 123 + G + R + +VFQ+YAL+PHM+V DN++FGL++R K RV +A ++ Sbjct: 62 LAGRDITHAKANTRGLGIVFQSYALFPHMTVADNVSFGLEMRKVPKAERKDRVAQALGLV 121 Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHR 183 L + R P +LSGGQRQRVA+ RA+V + V L+DEPLSNLDAKLR M+ E+ +I R Sbjct: 122 HLEKHAGRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDAKLREEMQFELRQIQR 181 Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVA 243 ++G TT+ VTHDQ+EAM+++DR+V+M + GR Q+ P +Y P +F++ Sbjct: 182 KVGTTTVMVTHDQSEAMSISDRVVVMEA----------GRATQIDHPHRVYEHPRTRFIS 231 Query: 244 GFIGSPAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKM-LESKGFK-NKNLIFGIRPEDIS 301 F+G + G + + V G +++ +E F+ ++ +RPE + Sbjct: 232 TFVGK-------ANLVPGQVTTASATHTHVGAGPIEVRVEGAQFRPGAAVLLSVRPEKLQ 284 Query: 302 SSLLVQETYPDATVDAEVVVSELLGSETMLYLKLGQTEF--AARVDARDFHEPGEKVSL 358 VQ +D EV LGS+ + + G + A D R E GE+ L Sbjct: 285 LVPTVQ-----GRIDGEVCERFFLGSQWLYRVGTGMGDLMVLAPNDGRGALEEGERTGL 338 Lambda K H 0.318 0.135 0.375 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: 305 Number of extensions: 12 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: 377 Length of database: 362 Length adjustment: 30 Effective length of query: 347 Effective length of database: 332 Effective search space: 115204 Effective search space used: 115204 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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