Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate PP_0879 PP_0879 dipeptide ABC transporter - putative ATP binding subunit
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__Putida:PP_0879 Length = 322 Score = 186 bits (473), Expect = 1e-51 Identities = 111/316 (35%), Positives = 178/316 (56%), Gaps = 6/316 (1%) Query: 7 SLLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPG 66 SLL++N L + + + + V ++ +V EI AI GESG GKS MA+ GL+ PG Sbjct: 2 SLLQINNLNVRFGDANAVPV-VDGLDLKVDAGEILAIVGESGSGKSVTMMALMGLIDAPG 60 Query: 67 VVLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH-G 125 + + D+L ++ + RK+ K+ V Q M AL+P +G Q+ H G Sbjct: 61 RITADSLTFDGTDMLKLSGRQRRKVVGKDIAMVFQDPMTALNPSYTVGFQIEEVLRQHLG 120 Query: 126 VNVEEARKLIKEKLELVDLPY--NVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPT 183 + + AR+ E L+ V++P + ++ YPH+LSGGM QRV IA +I P L+I DEPT Sbjct: 121 LKGKAARQRALELLKKVEIPAAESRLDAYPHQLSGGMSQRVAIAMAIAGEPKLLIADEPT 180 Query: 184 TGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEI 243 T LDV +Q +I++ L +Q++ ++L++I+HD++++ + RV +MYAG+ VE+G E+ Sbjct: 181 TALDVTIQAQIMELLVNLQKERNMALILITHDLAVVAETARRVCVMYAGQAVEVGQVPEL 240 Query: 244 IKRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTL 303 P+HPY+ L++++P E+L ++PG P + P C RCP+ + C Sbjct: 241 FDVPAHPYSEALLAAIPEHSIGAERLATLPGIVPGRYDR-PVGCLLSPRCPYVQDNCRRQ 299 Query: 304 NPALGDIMDGHKARCF 319 P L D RCF Sbjct: 300 RPPL-DPQAHSLVRCF 314 Score = 146 bits (369), Expect = 1e-39 Identities = 86/241 (35%), Positives = 138/241 (57%), Gaps = 7/241 (2%) Query: 378 INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQ----TSGKIILLGKDVSEY- 432 + V+ + ++ G I A+VG SG GKS L G+I T+ + G D+ + Sbjct: 19 VPVVDGLDLKVDAGEILAIVGESGSGKSVTMMALMGLIDAPGRITADSLTFDGTDMLKLS 78 Query: 433 GVRNSMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKNV 492 G + +++ M+FQDP ++L+P +TV + +E L H + K + +E+LK V Sbjct: 79 GRQRRKVVGKDIAMVFQDPMTALNPSYTVGFQIEEVLRQHLGLKGK-AARQRALELLKKV 137 Query: 493 GLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIKK 552 + E L YPH+LSGG QRVAIA A A EPK+L+ADEP + LD +++A I+ L+ Sbjct: 138 EIPAAESRLDAYPHQLSGGMSQRVAIAMAIAGEPKLLIADEPTTALDVTIQAQIMELLVN 197 Query: 553 F-KKNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAVP 611 K+ ++++ ITHD+A V A + V+Y G+ VE G E+ P+H Y++ L+ A+P Sbjct: 198 LQKERNMALILITHDLAVVAETARRVCVMYAGQAVEVGQVPELFDVPAHPYSEALLAAIP 257 Query: 612 D 612 + Sbjct: 258 E 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: 491 Number of extensions: 23 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: 322 Length adjustment: 32 Effective length of query: 585 Effective length of database: 290 Effective search space: 169650 Effective search space used: 169650 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