Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate Ac3H11_4785 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4785 Length = 334 Score = 305 bits (781), Expect = 1e-87 Identities = 182/381 (47%), Positives = 228/381 (59%), Gaps = 54/381 (14%) Query: 1 MTTLKLDNIYKRY---PNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDI 57 M +L L NI KRY P A + N ++ D EF+V VGPSGCGKST LRM+AGLE+I Sbjct: 1 MASLSLRNITKRYGHGPKANQV-IHGVNAEVKDGEFVVIVGPSGCGKSTLLRMVAGLEEI 59 Query: 58 TEGNLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVH 117 + G L I D+++ND P RDIAMVFQNYALYPHM+ +ENMA+GLK+ K KD+I RV Sbjct: 60 SGGELRIGDRVVNDLEPAQRDIAMVFQNYALYPHMTNFENMAYGLKIAKVPKDEIKARVD 119 Query: 118 EAAEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAE 177 +AA+IL L LERKP +LSGGQRQRVAMGRAIVR +VFL DEPLSNLDAKLR R E Sbjct: 120 KAAKILELGHLLERKPRELSGGQRQRVAMGRAIVRQPQVFLFDEPLSNLDAKLRAQTRLE 179 Query: 178 IAKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEP 237 I K+HR +G T+++VTHDQ EAMTLA R+++M+A G +EQ GTP+E+Y+ P Sbjct: 180 IQKLHRELGITSLFVTHDQVEAMTLAQRMIVMNA----------GNMEQFGTPEEVYHTP 229 Query: 238 ANKFVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRP 297 A FVA FIGSP MN L N G LGIRP Sbjct: 230 ATTFVASFIGSPPMNL---------LKNAPGAQ------------------PGTILGIRP 262 Query: 298 E--DISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARV-NARDSHSPGE 354 E D+ S+ +VT + + ELLG+E ++Y + + RV S P Sbjct: 263 EHLDVRSE--------GWAVTVETV--ELLGAERLIYGRINGEQVIVRVEEGTHSPEPDS 312 Query: 355 KVQLTFNIAKGHFFDLETEKR 375 + + + H FD T KR Sbjct: 313 VIHVQPRADRLHAFDAATGKR 333 Lambda K H 0.318 0.135 0.379 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: 356 Number of extensions: 18 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 377 Length of database: 334 Length adjustment: 29 Effective length of query: 348 Effective length of database: 305 Effective search space: 106140 Effective search space used: 106140 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