Align periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13) (characterized)
to candidate AZOBR_RS31645 AZOBR_RS31645 2-keto-gluconate dehydrogenase
Query= reanno::Pedo557:CA265_RS15345 (567 letters) >FitnessBrowser__azobra:AZOBR_RS31645 Length = 523 Score = 181 bits (460), Expect = 5e-50 Identities = 161/571 (28%), Positives = 236/571 (41%), Gaps = 81/571 (14%) Query: 17 IVIGSGISGGWAAKELTEKGLRVLMLERG--MNIEHITGYETAMKNPWDFKHAGKLTEEQ 74 +++GSG GG +L KG++ ++LE G N+E E A F L Sbjct: 14 VIVGSGAGGGTLGTQLALKGIKTVILEAGGRHNMEDFQNDEWA-----SFAQISWLDPRT 68 Query: 75 KRTHPVQKRDYPYQEANEKWWVNDLECPYTEDKRFDWYRGFHVGGKSLMWGRQSYRLSDH 134 RD+P A W V VGG ++ W + R H Sbjct: 69 TSGSWRVSRDFPGLPA---WIVKA------------------VGGSTVHWAGAALRFQPH 107 Query: 135 NFEDNARDGHGS-----DWPVRYAELSPWYDYAERFAGISGSKENWPTCPDGQFLPPMDL 189 F+ G + DWP+ EL PWY AE G++ + +P + Sbjct: 108 EFKTRTAYGEVAGANLLDWPITLEELEPWYAKAEDRMGVTRTNG----------IPGLPG 157 Query: 190 NIVEKSVKARIEEHYKRERIMMIGRVANLTVPHKGRGNCQYRNLCSRGCPFGAYFSTQSS 249 N K +KA ++ E G +A + P GRG CQ C +GC GA +ST + Sbjct: 158 NNNFKVLKAGADKMGYTE--CHTGNMAINSEPRDGRGGCQQIGFCFQGCKSGAKWSTLIA 215 Query: 250 TLPAAMATKRLTLRPYSIVNHIIYDKDTKKAKGVMVIDAETNKTMEFYAKIVFVNGSTLG 309 +P T +L +R + V I +D K GV+ D + A+IV V G+++ Sbjct: 216 EIPKGEETGKLEVRANAQVLKIEHDAKGK-VTGVVYADKD-GAIQRQKARIVAVAGNSIE 273 Query: 310 STFVLLNSTSEAHPNGLGNGSGQLGHNLMDHHFRCGASGEAEGFDDKYTYGRRANGIYIP 369 S +LLNS S P+GL N SGQ+G N M H +G G +K R + Sbjct: 274 SPRLLLNSASSMFPDGLANSSGQVGRNYMRH-----MTGSVYGVFEKPVRMYRGTTM--- 325 Query: 370 RYQNIGNDKRDYLRGFGYQGGASRANWQGDVAELSFGADLKQKMTTPGKW----SMGLGG 425 I D+ G+ GG ++ LS G PG W + L G Sbjct: 326 --AGIIRDEAKNKPDRGFVGGY-------EMETLSLGLPFMAAFLDPGAWGREFTSALDG 376 Query: 426 F---------GEMLPYYENKVYIDKTKKDKWGQPVLAIDCEYKENEKKMRVDMMNDAAEM 476 + GE +P N++ + KKDK G PV + + N+ MR + Sbjct: 377 YDHMAGMWLVGEDMPQESNRITLHADKKDKHGMPVPNVHFDDHPNDVAMRQHAYRQGMAL 436 Query: 477 LEKAGMKNIKTFDNGCYPGMAIHEMGTARMGNDPKTSVLNKWNQMHEVNNVFVTDGSCMP 536 E G ++F YP + H +GT RM + V+NKW Q H+V N+FV+DGS Sbjct: 437 YESVGAT--RSFPTPPYP--STHNLGTNRMSEKARDGVVNKWGQTHDVANLFVSDGSQFT 492 Query: 537 SIACQNPSLTFMALTARACDYAVKELKKKNI 567 + +NP+LT +AL R DY ++ K I Sbjct: 493 TGGAENPTLTIVALALRQADYIAGQMAKNAI 523 Lambda K H 0.317 0.134 0.421 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: 794 Number of extensions: 47 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: 567 Length of database: 523 Length adjustment: 35 Effective length of query: 532 Effective length of database: 488 Effective search space: 259616 Effective search space used: 259616 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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