Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate SMa0298 SMa0298 ABC transporter ATP-binding protein
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__Smeli:SMa0298 Length = 604 Score = 248 bits (632), Expect = 7e-70 Identities = 153/459 (33%), Positives = 244/459 (53%), Gaps = 17/459 (3%) Query: 5 MDSLLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKY 64 M +L++V L Y G+ V +V+FE+ P E F + GESGCGKST+A + G Sbjct: 1 MKNLIEVRNLNIAYGGPSGWTNVVQDVSFEIAPGEAFGLVGESGCGKSTVAYRLLGYGTI 60 Query: 65 PGVVLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH 124 +V G V D+L + L +LR +VPQ +L P ++G Q+ +H Sbjct: 61 NSLVQTGEVLFDGTDLLKLDAASLMRLRGNRIAFVPQNPTTSLSPGMRVGSQICEMIATH 120 Query: 125 -----GVNVEEARKLIKEKLELVDLPYNVVNMYPHELSGGMRQRVVIATSILLNPSLIIL 179 G+ +E + I E LV LP +V + YPHELSGG +QRV IA ++ NP L++L Sbjct: 121 KALPDGMTME---RRIVELFTLVGLP-DVGHRYPHELSGGQQQRVTIAMAVACNPDLLVL 176 Query: 180 DEPTTGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGS 239 DEPTTGLDV Q +I++ L ++ ++G++++ ++HD+++L I+DRVG+MYAG++VE+ Sbjct: 177 DEPTTGLDVTTQRQIIQLLADLRSRIGMAMLYVTHDLALLAQIADRVGVMYAGQLVEVAP 236 Query: 240 KEEIIKRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEK 299 ++++ P+HPY+ LI+S+P+ + S+ G L ++ C+F RC F Sbjct: 237 CDKLLSAPAHPYSRGLIASIPTNDGTDRQARSLRG--MLRRDEMSTGCKFEPRCDFATGA 294 Query: 300 CSTLNPALGDIMDGHKARCFLQKGGYVDLSTLPIPLEYYAEEKAETDLSESNQHEVVMKI 359 C L I D C + +T P+ A+ A T + + V Sbjct: 295 CRATPQLLELIEDARSVACMRWRE-----ATAPLAPSVTAKAVARTAVRSESLLSVTELS 349 Query: 360 LNLSKIYYIRKNLILSEPINAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQTS 419 L+ + + L + P V +++ L G + ALVGGSG GKSTIA+ ++ + + Sbjct: 350 LSYQQPGLFNRLLGRTSPA-VVREINLNLAAGEVVALVGGSGSGKSTIARAISARLPPRA 408 Query: 420 GKIILLGKDVSEYGVRNSMWYKENVQMIFQDPYSSLDPR 458 G I L G ++ S+ +Q IFQ+P +SL+PR Sbjct: 409 GIIRLDGTALAPSLKDRSVEELRQIQYIFQNPDASLNPR 447 Score = 140 bits (353), Expect = 2e-37 Identities = 87/240 (36%), Positives = 138/240 (57%), Gaps = 11/240 (4%) Query: 379 NAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGM-----IQQTSGKIILLGKDVSEYG 433 N V DVSFE+ G LVG SG GKST+A L G + QT G+++ G D+ + Sbjct: 22 NVVQDVSFEIAPGEAFGLVGESGCGKSTVAYRLLGYGTINSLVQT-GEVLFDGTDLLKLD 80 Query: 434 VRNSMWYKEN-VQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKNV 492 + M + N + + Q+P +SL P V + + HK + + + +I+E+ V Sbjct: 81 AASLMRLRGNRIAFVPQNPTTSLSPGMRVGSQICEMIATHKALPDGMTMERRIVELFTLV 140 Query: 493 GLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIKK 552 GL ++YPHELSGG++QRV IA A A P +LV DEP + LD + + I+ L+ Sbjct: 141 GLPDVG---HRYPHELSGGQQQRVTIAMAVACNPDLLVLDEPTTGLDVTTQRQIIQLLAD 197 Query: 553 FKKN-GISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAVP 611 + G+++LY+THD+A + IAD + V+Y G++VE +++S P+H Y++ LI ++P Sbjct: 198 LRSRIGMAMLYVTHDLALLAQIADRVGVMYAGQLVEVAPCDKLLSAPAHPYSRGLIASIP 257 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: 792 Number of extensions: 42 Number of successful extensions: 9 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: 604 Length adjustment: 37 Effective length of query: 580 Effective length of database: 567 Effective search space: 328860 Effective search space used: 328860 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: 53 (25.0 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