Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate WP_092483976.1 BM299_RS11015 ABC transporter ATP-binding protein
Query= TCDB::Q97UG5 (617 letters) >NCBI__GCF_900115975.1:WP_092483976.1 Length = 319 Score = 204 bits (518), Expect = 6e-57 Identities = 115/315 (36%), Positives = 177/315 (56%), Gaps = 4/315 (1%) Query: 8 LLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGV 67 LL + +L+ + G V + V+ V EI AI GESG GKS A++I GLL Sbjct: 2 LLDIKQLSVSFQTFQGSVHVLDRVSLSVDRGEILAIVGESGSGKSVTALSILGLLDKNAK 61 Query: 68 VLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSHG-V 126 + +G++ D+ ++ +E++K R K V Q M AL P +IGDQ+ H + Sbjct: 62 IEQGNIVFDGTDLTKLSTKEIQKYRGKRIGMVFQEPMTALHPTMRIGDQLTNVIKRHHKL 121 Query: 127 NVEEARKLIKEKLELVDL--PYNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTT 184 +E+ ++ E L+ V P + YPHELSGGMRQR+VIA ++ P L+I DEPTT Sbjct: 122 TKKESHPIMLEMLKDVHFEEPELIAQKYPHELSGGMRQRIVIALAMSAPPELLIADEPTT 181 Query: 185 GLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEII 244 LDV +Q EIL +K + ++ +++++I+HD+ ++ +SD V +MYAG+I+E G+ +EI+ Sbjct: 182 ALDVTIQAEILTLMKELTQKYNIAVILITHDLGVVREVSDNVCVMYAGKILEKGTTKEIL 241 Query: 245 KRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLN 304 P HPYT LL+ +LP V E+L I G P + +P C F RCP ++C Sbjct: 242 DNPKHPYTNLLLRALPDQVNPGERLQEIEGEVPDLKQHLP-GCIFSSRCPLSKDECFIKA 300 Query: 305 PALGDIMDGHKARCF 319 P + + C+ Sbjct: 301 PPQLSLSETQMVHCW 315 Score = 172 bits (437), Expect = 1e-47 Identities = 89/241 (36%), Positives = 150/241 (62%), Gaps = 7/241 (2%) Query: 378 INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQTS----GKIILLGKDVSEYG 433 ++ ++ VS + +G I A+VG SG GKS A + G++ + + G I+ G D+++ Sbjct: 19 VHVLDRVSLSVDRGEILAIVGESGSGKSVTALSILGLLDKNAKIEQGNIVFDGTDLTKLS 78 Query: 434 VRNSMWYK-ENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKNV 492 + Y+ + + M+FQ+P ++L P + + + H K++ K+ P ++E+LK+V Sbjct: 79 TKEIQKYRGKRIGMVFQEPMTALHPTMRIGDQLTNVIKRHHKLTKKESH-PIMLEMLKDV 137 Query: 493 GLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIKK 552 + PE KYPHELSGG RQR+ IA A + P++L+ADEP + LD +++A IL L+K+ Sbjct: 138 HFEEPELIAQKYPHELSGGMRQRIVIALAMSAPPELLIADEPTTALDVTIQAEILTLMKE 197 Query: 553 F-KKNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAVP 611 +K I+++ ITHD+ V ++D + V+Y G+I+EKG T E++ NP H YT L+ A+P Sbjct: 198 LTQKYNIAVILITHDLGVVREVSDNVCVMYAGKILEKGTTKEILDNPKHPYTNLLLRALP 257 Query: 612 D 612 D Sbjct: 258 D 258 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: 504 Number of extensions: 25 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: 319 Length adjustment: 32 Effective length of query: 585 Effective length of database: 287 Effective search space: 167895 Effective search space used: 167895 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