Align MalK, component of Maltose and maltooligosaccharide porter (characterized)
to candidate 17602 b3541 dipeptide transporter (NCBI)
Query= TCDB::Q97UG5 (617 letters) >FitnessBrowser__Keio:17602 Length = 327 Score = 210 bits (535), Expect = 6e-59 Identities = 113/315 (35%), Positives = 185/315 (58%), Gaps = 4/315 (1%) Query: 7 SLLKVNELTAGYFNQDGFVIGVTNVNFEVYPNEIFAIAGESGCGKSTLAMAIYGLLKYPG 66 +LL V++L+ + ++ V +++ V E+ I GESG GKS ++AI GL+ YPG Sbjct: 2 ALLNVDKLSVHFGDESAPFRAVDRISYSVKQGEVVGIVGESGSGKSVSSLAIMGLIDYPG 61 Query: 67 VVLRGHVYLKDKDILSITQEELRKLRMKEFVYVPQFAMDALDPVAKIGDQMMRAAVSH-G 125 V+ + +D+ I+++E R L E + Q M +L+P +G Q+M A H G Sbjct: 62 RVMAEKLEFNGQDLQRISEKERRNLVGAEVAMIFQDPMTSLNPCYTVGFQIMEAIKVHQG 121 Query: 126 VNVEEARKLIKEKLELVDLP--YNVVNMYPHELSGGMRQRVVIATSILLNPSLIILDEPT 183 N R+ + L V +P + +++YPH+LSGGM QRV+IA +I P L+I DEPT Sbjct: 122 GNKSTRRQRAIDLLNQVGIPDPASRLDVYPHQLSGGMSQRVMIAMAIACRPKLLIADEPT 181 Query: 184 TGLDVIVQYEILKDLKRIQRQLGVSLVIISHDISMLLMISDRVGIMYAGEIVEIGSKEEI 243 T LDV +Q +I++ L +Q++ ++LV+I+HD++++ + ++ +MYAG++VE G I Sbjct: 182 TALDVTIQAQIIELLLELQQKENMALVLITHDLALVAEAAHKIIVMYAGQVVETGDAHAI 241 Query: 244 IKRPSHPYTYLLISSLPSLVKRREKLLSIPGNPPLMLSKVPNSCRFYDRCPFKMEKCSTL 303 P HPYT L+ +LP + +E+L S+PG P + PN C RCP+ ++C Sbjct: 242 FHAPRHPYTQALLRALPEFAQDKERLASLPGVVPGKYDR-PNGCLLNPRCPYATDRCRAE 300 Query: 304 NPALGDIMDGHKARC 318 PAL + DG +++C Sbjct: 301 EPALNMLADGRQSKC 315 Score = 160 bits (405), Expect = 8e-44 Identities = 92/246 (37%), Positives = 148/246 (60%), Gaps = 11/246 (4%) Query: 375 SEPINAVNDVSFELKKGTITALVGGSGHGKSTIAKILAGMIQQT----SGKIILLGKD-- 428 S P AV+ +S+ +K+G + +VG SG GKS + + G+I + K+ G+D Sbjct: 17 SAPFRAVDRISYSVKQGEVVGIVGESGSGKSVSSLAIMGLIDYPGRVMAEKLEFNGQDLQ 76 Query: 429 -VSEYGVRNSMWYKENVQMIFQDPYSSLDPRHTVRWHVERPLLIHKKVSNKDQLLPKIIE 487 +SE RN + + V MIFQDP +SL+P +TV + + + +H+ NK + I+ Sbjct: 77 RISEKERRNLVGAE--VAMIFQDPMTSLNPCYTVGFQIMEAIKVHQG-GNKSTRRQRAID 133 Query: 488 VLKNVGLKPPEKYLYKYPHELSGGERQRVAIARATAVEPKVLVADEPVSMLDASLRAGIL 547 +L VG+ P L YPH+LSGG QRV IA A A PK+L+ADEP + LD +++A I+ Sbjct: 134 LLNQVGIPDPASRLDVYPHQLSGGMSQRVMIAMAIACRPKLLIADEPTTALDVTIQAQII 193 Query: 548 NLIKKF-KKNGISILYITHDIATVNYIADEIMVIYKGRIVEKGNTYEVISNPSHEYTKRL 606 L+ + +K ++++ ITHD+A V A +I+V+Y G++VE G+ + + P H YT+ L Sbjct: 194 ELLLELQQKENMALVLITHDLALVAEAAHKIIVMYAGQVVETGDAHAIFHAPRHPYTQAL 253 Query: 607 IEAVPD 612 + A+P+ Sbjct: 254 LRALPE 259 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: 510 Number of extensions: 30 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: 327 Length adjustment: 33 Effective length of query: 584 Effective length of database: 294 Effective search space: 171696 Effective search space used: 171696 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