Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate 1936449 b1246 oligopeptide transporter ATP-binding component (NCBI)
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__Keio:1936449 Length = 337 Score = 221 bits (562), Expect = 5e-62 Identities = 122/317 (38%), Positives = 187/317 (58%), Gaps = 6/317 (1%) Query: 6 DSLLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYP 65 D+LL V +L + DG V V ++NF + E I GESG GKS A A+ GLL Sbjct: 17 DALLNVKDLRVTFSTPDGDVTAVNDLNFSLRAGETLGIVGESGSGKSQTAFALMGLLAAN 76 Query: 66 GVVLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH- 124 G + G ++IL++ + EL KLR ++ + Q M +L+P ++G+Q+M + H Sbjct: 77 GRI-GGSATFNGREILNLPEHELNKLRAEQISMIFQDPMTSLNPYMRVGEQLMEVLMLHK 135 Query: 125 GVNVEEARKLIKEKLELVDLPY--NVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEP 182 ++ EA + L+ V +P + MYPHE SGGMRQRV+IA ++L P L+I DEP Sbjct: 136 NMSKAEAFEESVRMLDAVKMPEARKRMKMYPHEFSGGMRQRVMIAMALLCRPKLLIADEP 195 Query: 183 TTGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEE 242 TT LDV VQ +I+ L ++R+ ++++I+HD+ ++ I D+V +MYAG +E G+ + Sbjct: 196 TTALDVTVQAQIMTLLNELKREFNTAIIMITHDLVVVAGICDKVLVMYAGRTMEYGNARD 255 Query: 243 IIKRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCST 302 + +P HPY+ L++++P L E +L+IPGNPP +L ++P C F RCP ME CS+ Sbjct: 256 VFYQPVHPYSIGLLNAVPRLDAEGETMLTIPGNPPNLL-RLPKGCPFQPRCPHAMEICSS 314 Query: 303 LNPALGDIMDGHKARCF 319 P L + G CF Sbjct: 315 A-PPLEEFTPGRLRACF 330 Score = 152 bits (383), Expect = 3e-41 Identities = 88/239 (36%), Positives = 134/239 (56%), Gaps = 6/239 (2%) Query: 378 INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQ---QTSGKIILLGKDVSEYGV 434 + AVND++F L+ G +VG SG GKS A L G++ + G G+++ Sbjct: 36 VTAVNDLNFSLRAGETLGIVGESGSGKSQTAFALMGLLAANGRIGGSATFNGREILNLPE 95 Query: 435 RN-SMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKNVG 493 + E + MIFQDP +SL+P V + L++HK +S K + + + +L V Sbjct: 96 HELNKLRAEQISMIFQDPMTSLNPYMRVGEQLMEVLMLHKNMS-KAEAFEESVRMLDAVK 154 Query: 494 LKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLIKKF 553 + K + YPHE SGG RQRV IA A PK+L+ADEP + LD +++A I+ L+ + Sbjct: 155 MPEARKRMKMYPHEFSGGMRQRVMIAMALLCRPKLLIADEPTTALDVTVQAQIMTLLNEL 214 Query: 554 KKN-GISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEAVP 611 K+ +I+ ITHD+ V I D+++V+Y GR +E GN +V P H Y+ L+ AVP Sbjct: 215 KREFNTAIIMITHDLVVVAGICDKVLVMYAGRTMEYGNARDVFYQPVHPYSIGLLNAVP 273 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: 500 Number of extensions: 21 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: 337 Length adjustment: 33 Effective length of query: 584 Effective length of database: 304 Effective search space: 177536 Effective search space used: 177536 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