Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate WP_092481461.1 BM299_RS19630 ABC transporter ATP-binding protein
Query= TCDB::Q97UG5 (617 letters) >NCBI__GCF_900115975.1:WP_092481461.1 Length = 326 Score = 214 bits (545), Expect = 4e-60 Identities = 118/321 (36%), Positives = 188/321 (58%), Gaps = 5/321 (1%) Query: 8 LLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYP-G 66 LL V +L +F DG V V V+F + E A+ GESG GKS +++I L+ P G Sbjct: 5 LLNVEDLKTHFFLDDGVVPAVDGVSFHLRKGETLAVVGESGSGKSITSLSIMRLVPAPPG 64 Query: 67 VVLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSHG- 125 ++ G + +D+L+ +++E+R +R + Q M +L+PV ++GDQ+ + V H Sbjct: 65 RIVGGRITFAGEDLLAKSEKEMRDVRGNRISMIFQEPMTSLNPVYRVGDQIAESLVLHKR 124 Query: 126 VNVEEARKLIKEKLELVDLPY--NVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPT 183 + +EA + E L L +P V +PH++SGGMRQRV+IA ++ P L+I DEPT Sbjct: 125 MKKKEALEQAVEMLRLTGIPSPEKRVRDFPHQMSGGMRQRVMIAMALCCQPELLIADEPT 184 Query: 184 TGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEI 243 T LDV +Q +IL+ ++ +QRQ+ S+++I+HD++++ ++DR +MY G++VE E+ Sbjct: 185 TALDVTIQAQILELMQELQRQMNTSIILITHDLAVVAEVADRAVVMYCGKVVEEAPVAEL 244 Query: 244 IKRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTL 303 + P HPYT L++S+P L + ++L I G P ML ++P C F RCP E C Sbjct: 245 FENPLHPYTRGLLNSIPRLDENVDRLFMIDGVVPNML-RLPPGCAFAPRCPEAREHCRET 303 Query: 304 NPALGDIMDGHKARCFLQKGG 324 P L + G C L +GG Sbjct: 304 APRLTRVAPGRLVSCLLVEGG 324 Score = 163 bits (413), Expect = 9e-45 Identities = 88/241 (36%), Positives = 148/241 (61%), Gaps = 8/241 (3%) Query: 378 INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQTSGKII-----LLGKDVSEY 432 + AV+ VSF L+KG A+VG SG GKS + + ++ G+I+ G+D+ Sbjct: 22 VPAVDGVSFHLRKGETLAVVGESGSGKSITSLSIMRLVPAPPGRIVGGRITFAGEDLLAK 81 Query: 433 GVRNSMWYKEN-VQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKN 491 + + N + MIFQ+P +SL+P + V + L++HK++ K+ L + +E+L+ Sbjct: 82 SEKEMRDVRGNRISMIFQEPMTSLNPVYRVGDQIAESLVLHKRMKKKEAL-EQAVEMLRL 140 Query: 492 VGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIK 551 G+ PEK + +PH++SGG RQRV IA A +P++L+ADEP + LD +++A IL L++ Sbjct: 141 TGIPSPEKRVRDFPHQMSGGMRQRVMIAMALCCQPELLIADEPTTALDVTIQAQILELMQ 200 Query: 552 KFKKN-GISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAV 610 + ++ SI+ ITHD+A V +AD +V+Y G++VE+ E+ NP H YT+ L+ ++ Sbjct: 201 ELQRQMNTSIILITHDLAVVAEVADRAVVMYCGKVVEEAPVAELFENPLHPYTRGLLNSI 260 Query: 611 P 611 P Sbjct: 261 P 261 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: 419 Number of extensions: 20 Number of successful extensions: 8 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