Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate BWI76_RS26870 BWI76_RS26870 dipeptide ABC transporter ATP-binding protein
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__Koxy:BWI76_RS26870 Length = 327 Score = 204 bits (519), Expect = 5e-57 Identities = 109/317 (34%), Positives = 189/317 (59%), Gaps = 8/317 (2%) Query: 7 SLLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPG 66 +LL V++L+ + ++ V V++ V E+ I GESG GKS ++AI GL+ YPG Sbjct: 2 ALLNVDKLSVHFGDEGTPFRAVDRVSYSVNQGEVVGIVGESGSGKSVSSLAIMGLIDYPG 61 Query: 67 VVLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSHGV 126 V+ + +D+ I+++E R+L E + Q M +L+P +G Q+M A H Sbjct: 62 RVMAEKLEFNGRDLKRISEKERRQLVGAEVAMIFQDPMTSLNPCYTVGYQIMEAIKVHQG 121 Query: 127 NVEEARKLIKEKLELVDL-----PYNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDE 181 ++ R I+ ++L+ L P + +++YPH+LSGGM QRV+IA +I P L+I DE Sbjct: 122 GNKKTR--IQRAIDLLTLVGIPDPASRLDVYPHQLSGGMSQRVMIAMAIACRPKLLIADE 179 Query: 182 PTTGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKE 241 PTT LDV +Q +I++ L +Q++ ++L++I+HD++++ + ++ +MYAG++VE G + Sbjct: 180 PTTALDVTIQAQIIELLLELQQKENMALILITHDLALVAEAAHKIIVMYAGQVVETGDAK 239 Query: 242 EIIKRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCS 301 +I + P HPYT L+ +LP + + +L S+PG P + P+ C RCP+ +KC Sbjct: 240 DIFRAPRHPYTQALLRALPEFAQDKARLASLPGVVPGKYDR-PSGCLLNPRCPYATDKCR 298 Query: 302 TLNPALGDIMDGHKARC 318 + P L + G +++C Sbjct: 299 SEEPELNLLNGGRQSKC 315 Score = 156 bits (395), Expect = 1e-42 Identities = 87/242 (35%), Positives = 142/242 (58%), Gaps = 7/242 (2%) Query: 377 PINAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQT----SGKIILLGKDVSEY 432 P AV+ VS+ + +G + +VG SG GKS + + G+I + K+ G+D+ Sbjct: 19 PFRAVDRVSYSVNQGEVVGIVGESGSGKSVSSLAIMGLIDYPGRVMAEKLEFNGRDLKRI 78 Query: 433 GVRNS-MWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKN 491 + V MIFQDP +SL+P +TV + + + +H+ NK + + I++L Sbjct: 79 SEKERRQLVGAEVAMIFQDPMTSLNPCYTVGYQIMEAIKVHQG-GNKKTRIQRAIDLLTL 137 Query: 492 VGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIK 551 VG+ P L YPH+LSGG QRV IA A A PK+L+ADEP + LD +++A I+ L+ Sbjct: 138 VGIPDPASRLDVYPHQLSGGMSQRVMIAMAIACRPKLLIADEPTTALDVTIQAQIIELLL 197 Query: 552 KF-KKNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAV 610 + +K ++++ ITHD+A V A +I+V+Y G++VE G+ ++ P H YT+ L+ A+ Sbjct: 198 ELQQKENMALILITHDLALVAEAAHKIIVMYAGQVVETGDAKDIFRAPRHPYTQALLRAL 257 Query: 611 PD 612 P+ Sbjct: 258 PE 259 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: 27 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: 327 Length adjustment: 33 Effective length of query: 584 Effective length of database: 294 Effective search space: 171696 Effective search space used: 171696 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 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