Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate Pf1N1B4_1127 Dipeptide transport ATP-binding protein DppF (TC 3.A.1.5.2)
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1127 Length = 326 Score = 191 bits (484), Expect = 5e-53 Identities = 106/267 (39%), Positives = 168/267 (62%), Gaps = 9/267 (3%) Query: 355 VVMKILNLSKIYYIRKNLILSEP-INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAG 413 VV+ NL++ Y + + L + A+N VSFEL+ G A+VG SG GKST+A+ L Sbjct: 3 VVLTARNLTRHYEVSRGLFKGHATVRALNGVSFELEAGKTLAVVGESGCGKSTLARALTL 62 Query: 414 MIQQTSGKIILLGKDVSEYGVRNSMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIHK 473 + + +SG + + G++V+ +++VQM+FQ PY+SL+PR V + PLLI+ Sbjct: 63 IEEPSSGSLKIAGQEVAGADKAQRKQLRKDVQMVFQSPYASLNPRQKVGDQLAEPLLINT 122 Query: 474 KVSNKDQLLPKIIEVLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADE 533 +S ++ K+ ++K VGL+P ++ +YPH SGG+RQR+A+ARA ++PKVLVADE Sbjct: 123 NLSASER-REKVQAMMKQVGLRP--EHYQRYPHMFSGGQRQRIALARAMMLQPKVLVADE 179 Query: 534 PVSMLDASLRAGILNLIKKFKKN-GISILYITHDIATVNYIADEIMVIYKGRIVEKGNTY 592 P S LD S++A +LNL ++ + ++I+H++A V ++AD +MV+Y GR VE G Sbjct: 180 PTSALDVSIQAQVLNLFMDLQQEFNTAYVFISHNLAVVRHVADHVMVMYLGRPVEMGPKE 239 Query: 593 EVISNPSHEYTKRLIEAV----PDPYK 615 ++ + P H YT+ L+ A PDP K Sbjct: 240 DIYTRPLHPYTQALLSATPTIHPDPTK 266 Score = 176 bits (447), Expect = 1e-48 Identities = 102/314 (32%), Positives = 178/314 (56%), Gaps = 9/314 (2%) Query: 7 SLLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPG 66 +L + E++ G F V + V+FE+ + A+ GESGCGKSTLA A+ L++ P Sbjct: 9 NLTRHYEVSRGLFKGHATVRALNGVSFELEAGKTLAVVGESGCGKSTLARALT-LIEEPS 67 Query: 67 VVLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAA-VSHG 125 G + + +++ + + ++LR K+ V Q +L+P K+GDQ+ ++ Sbjct: 68 ---SGSLKIAGQEVAGADKAQRKQLR-KDVQMVFQSPYASLNPRQKVGDQLAEPLLINTN 123 Query: 126 VNVEEARKLIKEKLELVDLPYNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTTG 185 ++ E R+ ++ ++ V L YPH SGG RQR+ +A +++L P +++ DEPT+ Sbjct: 124 LSASERREKVQAMMKQVGLRPEHYQRYPHMFSGGQRQRIALARAMMLQPKVLVADEPTSA 183 Query: 186 LDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEIIK 245 LDV +Q ++L +Q++ + V ISH+++++ ++D V +MY G VE+G KE+I Sbjct: 184 LDVSIQAQVLNLFMDLQQEFNTAYVFISHNLAVVRHVADHVMVMYLGRPVEMGPKEDIYT 243 Query: 246 RPSHPYTYLLISSLPSLVKRREK-LLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLN 304 RP HPYT L+S+ P++ K + I G P L+ P+ C F+ RCP+ ++C+T Sbjct: 244 RPLHPYTQALLSATPTIHPDPTKPKIKIVGELPNPLNP-PSGCAFHKRCPYATDRCTTEE 302 Query: 305 PALGDIMDGHKARC 318 P L ++D + C Sbjct: 303 PLL-RLVDTRQVAC 315 Lambda K H 0.319 0.138 0.391 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: 502 Number of extensions: 22 Number of successful extensions: 7 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: 617 Length of database: 326 Length adjustment: 33 Effective length of query: 584 Effective length of database: 293 Effective search space: 171112 Effective search space used: 171112 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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