Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate 8500263 DvMF_1020 oligopeptide/dipeptide ABC transporter, ATPase subunit (RefSeq)
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__Miya:8500263 Length = 358 Score = 192 bits (488), Expect = 2e-53 Identities = 104/285 (36%), Positives = 167/285 (58%), Gaps = 6/285 (2%) Query: 28 VTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGVVLRGHVYLKDKDILSITQEE 87 V ++F + P + GESGCGKS A+A+ L+ PG V G V L+ +++L++ + E Sbjct: 44 VAGISFSIAPGGTLCLVGESGCGKSMTALALLRLVPEPGRVASGSVRLEGRELLTLPEPE 103 Query: 88 LRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH-GVNVEEARKLIKEKLELVDLPY 146 +R +R + + Q M +L+PV ++G+Q+ H G++ +A + L V +P Sbjct: 104 MRGVRGRSISMIFQEPMTSLNPVFRVGEQIAEGVRLHLGLSRSDAAARAVDLLRQVGIPS 163 Query: 147 NVVNM--YPHELSGGMRQRVVIATSILLNPSLIILDEPTTGLDVIVQYEILKDLKRIQRQ 204 + +PH++SGGMRQRV+IA ++ +P L+I DEPTT LDV +Q +IL+ ++ + Sbjct: 164 PELRARDFPHQMSGGMRQRVMIAMALACDPRLLIADEPTTALDVTIQRQILRLMRDLAAH 223 Query: 205 LGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEIIKRPSHPYTYLLISSLPSLVK 264 G S+++I+HD+ ++ +D V +MYAG I+E S + RP HPY L+ S+P V Sbjct: 224 RGASVLLITHDLGVVAETADHVAVMYAGRIMEHASVGDFFARPLHPYAQGLMRSVPQAVS 283 Query: 265 --RREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTLNPAL 307 R E+L +IPG P L +P+ C F DRCP +C+ P L Sbjct: 284 GPRAERLSAIPGTVP-PLWALPSGCTFRDRCPHAFARCAEQEPPL 327 Score = 144 bits (362), Expect = 8e-39 Identities = 86/246 (34%), Positives = 136/246 (55%), Gaps = 17/246 (6%) Query: 377 PINAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQ----TSGKIILLGKDVSEY 432 P+ AV +SF + G LVG SG GKS A L ++ + SG + L G+++ Sbjct: 40 PLRAVAGISFSIAPGGTLCLVGESGCGKSMTALALLRLVPEPGRVASGSVRLEGRELLTL 99 Query: 433 ------GVRNSMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKII 486 GVR ++ MIFQ+P +SL+P V + + +H +S D + + Sbjct: 100 PEPEMRGVRG-----RSISMIFQEPMTSLNPVFRVGEQIAEGVRLHLGLSRSDAAA-RAV 153 Query: 487 EVLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGI 546 ++L+ VG+ PE +PH++SGG RQRV IA A A +P++L+ADEP + LD +++ I Sbjct: 154 DLLRQVGIPSPELRARDFPHQMSGGMRQRVMIAMALACDPRLLIADEPTTALDVTIQRQI 213 Query: 547 LNLIKKFKKN-GISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKR 605 L L++ + G S+L ITHD+ V AD + V+Y GRI+E + + + P H Y + Sbjct: 214 LRLMRDLAAHRGASVLLITHDLGVVAETADHVAVMYAGRIMEHASVGDFFARPLHPYAQG 273 Query: 606 LIEAVP 611 L+ +VP Sbjct: 274 LMRSVP 279 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: 447 Number of extensions: 17 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: 358 Length adjustment: 33 Effective length of query: 584 Effective length of database: 325 Effective search space: 189800 Effective search space used: 189800 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