Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate Ac3H11_2051 Oligopeptide transport system permease protein OppB (TC 3.A.1.5.1)
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2051 Length = 348 Score = 212 bits (540), Expect = 2e-59 Identities = 119/326 (36%), Positives = 189/326 (57%), Gaps = 9/326 (2%) Query: 3 EIMDSLLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLL 62 +I SLL+V L + + G + + +++F + P EI + GESG GKS AI GLL Sbjct: 9 DIPMSLLEVKNLVVEFPGRRGTLRALDDISFSIAPGEILGVVGESGAGKSLTGAAIIGLL 68 Query: 63 KYPGVVLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAV 122 + PG V G + L+ + I +++ EE+R +R + + Q + +L+P+ +G Q+ + Sbjct: 69 EPPGRVASGQILLEGQRIDNLSNEEMRHIRGRRIGAIFQDPLTSLNPLYTVGRQLTETIL 128 Query: 123 SH-GVNVEEARKLIKEKLELVDLPY--NVVNMYPHELSGGMRQRVVIATSILLNPSLIIL 179 +H V EAR+ L+ +P ++ YPH+ SGGMRQRVVIA ++ P LI+ Sbjct: 129 AHLPVTPAEARQRAIALLKDTGIPAAEERIDHYPHQFSGGMRQRVVIALALAAEPKLIVA 188 Query: 180 DEPTTGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGS 239 DEPTT LDV +Q +I+ LK I + G ++++I+HD+ ++ DRV ++YAG + EIG Sbjct: 189 DEPTTALDVSIQAQIITLLKNICKSRGAAVMLITHDMGVIAETCDRVAVLYAGRVAEIGP 248 Query: 240 KEEIIKRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEK 299 ++I +PSHPYT L++S+P + RE+L I G P L+ +P C + RCP ++ Sbjct: 249 VHDVINKPSHPYTSGLMASIPDMTMDRERLNQIDGAMP-RLNAIPKGCAYNPRCPQTFDR 307 Query: 300 CSTLNPALGDIM--DGHKARCFLQKG 323 C T P D+M +A C+L G Sbjct: 308 CMTERP---DLMPAGSTRAACWLHAG 330 Score = 166 bits (420), Expect = 1e-45 Identities = 93/254 (36%), Positives = 146/254 (57%), Gaps = 12/254 (4%) Query: 370 KNLILSEP-----INAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQ----TSG 420 KNL++ P + A++D+SF + G I +VG SG GKS + G+++ SG Sbjct: 18 KNLVVEFPGRRGTLRALDDISFSIAPGEILGVVGESGAGKSLTGAAIIGLLEPPGRVASG 77 Query: 421 KIILLGKDVSEYGVRNSMWYK-ENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKD 479 +I+L G+ + + + IFQDP +SL+P +TV + +L H V+ + Sbjct: 78 QILLEGQRIDNLSNEEMRHIRGRRIGAIFQDPLTSLNPLYTVGRQLTETILAHLPVTPAE 137 Query: 480 QLLPKIIEVLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLD 539 + I +LK+ G+ E+ + YPH+ SGG RQRV IA A A EPK++VADEP + LD Sbjct: 138 AR-QRAIALLKDTGIPAAEERIDHYPHQFSGGMRQRVVIALALAAEPKLIVADEPTTALD 196 Query: 540 ASLRAGILNLIKKF-KKNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNP 598 S++A I+ L+K K G +++ ITHD+ + D + V+Y GR+ E G ++VI+ P Sbjct: 197 VSIQAQIITLLKNICKSRGAAVMLITHDMGVIAETCDRVAVLYAGRVAEIGPVHDVINKP 256 Query: 599 SHEYTKRLIEAVPD 612 SH YT L+ ++PD Sbjct: 257 SHPYTSGLMASIPD 270 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: 474 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: 348 Length adjustment: 33 Effective length of query: 584 Effective length of database: 315 Effective search space: 183960 Effective search space used: 183960 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