Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate 208073 DVU2576 oligopeptide ABC transporter, ATP-binding protein
Query= TCDB::Q97UG5 (617 letters) >MicrobesOnline__882:208073 Length = 321 Score = 182 bits (461), Expect = 2e-50 Identities = 118/317 (37%), Positives = 170/317 (53%), Gaps = 6/317 (1%) Query: 8 LLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPGV 67 LL+V L + + G + V +V+F + I GESGCGKS A+A+ GL+ PG Sbjct: 5 LLEVQGLDVVFDIEAGAIHAVRDVSFTLPHGRTLCIVGESGCGKSMTALALLGLVPAPGR 64 Query: 68 VLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH-GV 126 V + D+ ++ + LR LR V Q M +L+PV ++GDQ+ A H + Sbjct: 65 VTARRLQFDGHDLTALDENGLRALRGHHMAMVFQDPMTSLNPVFRVGDQVAEALRLHLRL 124 Query: 127 NVEEARKLIKEKLELVDLPYNVVNM--YPHELSGGMRQRVVIATSILLNPSLIILDEPTT 184 AR+ E V +P YPH+LSGGMRQRV+IA ++ P L+I DEPTT Sbjct: 125 KGRAAREATIELFRQVGIPSPETRYDDYPHQLSGGMRQRVMIAMALSCGPRLLIADEPTT 184 Query: 185 GLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEII 244 LDV +Q +IL L I S+++I+HD+ ++ +D V +MYAG IVE +E+ Sbjct: 185 ALDVTIQGQILGLLSDIAATGRASVLLITHDLGVVAETADDVIVMYAGAIVEHAPVQELF 244 Query: 245 KRPSHPYTYLLISSLPSL-VKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTL 303 P HPYT L+ S P + +R +L +I GN P L +P+ C F DRC E+C+T Sbjct: 245 ASPLHPYTRGLMRSAPPVHGERSPRLEAIRGNVP-PLDDLPSGCAFRDRCEHAFERCATA 303 Query: 304 NPALGDIMDGHKARCFL 320 P L + RC+L Sbjct: 304 APPL-FTLGKQMVRCWL 319 Score = 147 bits (372), Expect = 5e-40 Identities = 91/242 (37%), Positives = 137/242 (56%), Gaps = 11/242 (4%) Query: 378 INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMI----QQTSGKIILLGKDVS--- 430 I+AV DVSF L G +VG SG GKS A L G++ + T+ ++ G D++ Sbjct: 22 IHAVRDVSFTLPHGRTLCIVGESGCGKSMTALALLGLVPAPGRVTARRLQFDGHDLTALD 81 Query: 431 EYGVRNSMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIEVLK 490 E G+R + ++ M+FQDP +SL+P V V L +H ++ + IE+ + Sbjct: 82 ENGLRALRGH--HMAMVFQDPMTSLNPVFRVGDQVAEALRLHLRLKGR-AAREATIELFR 138 Query: 491 NVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGILNLI 550 VG+ PE YPH+LSGG RQRV IA A + P++L+ADEP + LD +++ IL L+ Sbjct: 139 QVGIPSPETRYDDYPHQLSGGMRQRVMIAMALSCGPRLLIADEPTTALDVTIQGQILGLL 198 Query: 551 KKFKKNG-ISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRLIEA 609 G S+L ITHD+ V AD+++V+Y G IVE E+ ++P H YT+ L+ + Sbjct: 199 SDIAATGRASVLLITHDLGVVAETADDVIVMYAGAIVEHAPVQELFASPLHPYTRGLMRS 258 Query: 610 VP 611 P Sbjct: 259 AP 260 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: 432 Number of extensions: 22 Number of successful extensions: 6 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: 321 Length adjustment: 32 Effective length of query: 585 Effective length of database: 289 Effective search space: 169065 Effective search space used: 169065 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