Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate BWI76_RS17225 BWI76_RS17225 oligopeptide ABC transporter ATP-binding protein OppD
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__Koxy:BWI76_RS17225 Length = 337 Score = 219 bits (559), Expect = 1e-61 Identities = 123/319 (38%), Positives = 186/319 (58%), Gaps = 6/319 (1%) Query: 8 LLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGV 67 LL V +L + DG V V ++NF + E I GESG GKS A A+ GLL G Sbjct: 19 LLDVKDLRVTFGTPDGDVTAVNDLNFNLRAGETLGIVGESGSGKSQTAFALMGLLAANGR 78 Query: 68 VLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH-GV 126 + G K IL++ + EL KLR ++ + Q M +L+P ++G+Q+M + H + Sbjct: 79 I-GGSATFNGKQILNLPERELNKLRAEQISMIFQDPMTSLNPYMRVGEQLMEVLMLHKAL 137 Query: 127 NVEEARKLIKEKLELVDLPY--NVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPTT 184 + EA + + L+ V +P + MYPHE SGGMRQRV+IA ++L P L+I DEPTT Sbjct: 138 SKAEAFEESVKMLDAVKMPEARKRMKMYPHEFSGGMRQRVMIAMALLCRPKLLIADEPTT 197 Query: 185 GLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEII 244 LDV VQ +I+ L ++R+ ++++I+HD+ ++ I D+V +MYAG +E G ++ Sbjct: 198 ALDVTVQAQIMTLLNELKREFNTAIIMITHDLGVVAGICDKVLVMYAGRTMEYGQARDVF 257 Query: 245 KRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLN 304 +PSHPY+ L++++P L + LL+IPGNPP +L ++P C F RCP ME C++ Sbjct: 258 YQPSHPYSIGLLNAVPRLDAEGDALLTIPGNPPNLL-RLPKGCPFQPRCPHAMEICNSA- 315 Query: 305 PALGDIMDGHKARCFLQKG 323 P L + G CF G Sbjct: 316 PPLEEFAPGRLRACFQPVG 334 Score = 154 bits (389), Expect = 6e-42 Identities = 90/239 (37%), Positives = 135/239 (56%), Gaps = 6/239 (2%) Query: 378 INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQ---QTSGKIILLGKDVSEYGV 434 + AVND++F L+ G +VG SG GKS A L G++ + G GK + Sbjct: 36 VTAVNDLNFNLRAGETLGIVGESGSGKSQTAFALMGLLAANGRIGGSATFNGKQILNLPE 95 Query: 435 RN-SMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLKNVG 493 R + E + MIFQDP +SL+P V + L++HK +S K + + +++L V Sbjct: 96 RELNKLRAEQISMIFQDPMTSLNPYMRVGEQLMEVLMLHKALS-KAEAFEESVKMLDAVK 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 G +V PSH Y+ L+ AVP Sbjct: 215 KREFNTAIIMITHDLGVVAGICDKVLVMYAGRTMEYGQARDVFYQPSHPYSIGLLNAVP 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: 485 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