Align periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13) (characterized)
to candidate CCNA_01706 CCNA_01706 BetA-family choline dehydrogenase
Query= reanno::Pedo557:CA265_RS15345 (567 letters) >FitnessBrowser__Caulo:CCNA_01706 Length = 579 Score = 629 bits (1621), Expect = 0.0 Identities = 315/577 (54%), Positives = 401/577 (69%), Gaps = 14/577 (2%) Query: 1 MMNLNTNLKAENTYDAIVIGSGISGGWAAKELTEKGLRVLMLERGMNIEHITGYETAMKN 60 M NLN + +NTYDAIV+GSGI+GG AAKELTEKGL+VL+LERG + H+ Y TAM + Sbjct: 1 MANLNGRARRKNTYDAIVVGSGITGGIAAKELTEKGLKVLVLERGPMVRHLEDYPTAMLD 60 Query: 61 PWDFKHA-GKLTEEQKRTH-PVQKRD-YPYQEANEKWWVNDLECPYTEDKRFDWYRGFHV 117 PW K+ GKL E + H VQ+R Y E + ++V D E PYTE+ RFDW RG+HV Sbjct: 61 PWQSKYPQGKLPEAELNAHYKVQRRTGYTMTEQTQHFFVRDDEHPYTEENRFDWIRGYHV 120 Query: 118 GGKSLMWGRQSYRLSDHNFEDNARDGHGSDWPVRYAELSPWYDYAERFAGISGSKENWPT 177 GG+SL WGRQSYR S +FE NAR+G DWP+RY +L+PWY++ ERF G+SG E P Sbjct: 121 GGRSLTWGRQSYRHSPIDFEANAREGIAVDWPIRYEDLAPWYEHVERFIGVSGQAEGLPH 180 Query: 178 CPDGQFLPPMDLNIVEKSVKARIEEHYKRERIMMIGRVANLTVPHK-----GRGNCQYRN 232 PDG + PPM+LN VEK+ KAR E + R+ IGR A+LT P + GR CQYRN Sbjct: 181 FPDGHYQPPMELNCVEKAFKARSEARFPERRVT-IGRTAHLTDPTEEQLALGRTKCQYRN 239 Query: 233 LCSRGCPFGAYFSTQSSTLPAAMATKRLTLRPYSIVNHIIYDKDTKKAKGVMVIDAETNK 292 LC RGCPFGAY+S+ S L AA T L +RP SIV +IYD+ +A GV ++DAET K Sbjct: 240 LCIRGCPFGAYYSSNSGGLIAAERTGNLVIRPNSIVTELIYDERAGRASGVRILDAETRK 299 Query: 293 TMEFYAKIVFVNGSTLGSTFVLLNSTSEAHPNGLGNGSGQLGHNLMDHHFRCGASGEAEG 352 EF+A ++F+ S L S ++++NSTS PNG GN S QLG N+MDHH GA+G+A Sbjct: 300 DEEFHADVIFLCASALNSAWIMMNSTSSRFPNGFGNASDQLGRNVMDHHLGAGATGQAPE 359 Query: 353 FDDKYTYGRRANGIYIPRYQNIGN---DKRDYLRGFGYQGGASRANWQGDVAE--LSFGA 407 F D Y GRR NGIY+PR++N+G+ + DYLRGFGYQGGA RA W+ D + FGA Sbjct: 360 FADMYFSGRRPNGIYVPRFRNLGDAASKRSDYLRGFGYQGGAGRATWERDRGQGGRGFGA 419 Query: 408 DLKQKMTTPGKWSMGLGGFGEMLPYYENKVYIDKTKKDKWGQPVLAIDCEYKENEKKMRV 467 K ++ PG W+MGL GFGEMLPY +N+V +++ +DK+G P L ++ ++NE MR Sbjct: 420 ARKAALSQPGPWTMGLSGFGEMLPYADNRVTLNRDVEDKFGLPTLTMNVTMRDNEMAMRR 479 Query: 468 DMMNDAAEMLEKAGMKNIKTFDNGCYPGMAIHEMGTARMGNDPKTSVLNKWNQMHEVNNV 527 DM AAEMLE AG +N++ DNG PG+ IHEMGTARMG DPKTSVLN NQ+HE NV Sbjct: 480 DMQAAAAEMLEAAGFQNVRAHDNGFAPGLGIHEMGTARMGRDPKTSVLNAHNQVHECKNV 539 Query: 528 FVTDGSCMPSIACQNPSLTFMALTARACDYAVKELKK 564 +VTDG+ M S +C NPSLT+MALTARA D+AV+ K+ Sbjct: 540 YVTDGAAMASASCVNPSLTYMALTARAADHAVRARKR 576 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: 991 Number of extensions: 39 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 567 Length of database: 579 Length adjustment: 36 Effective length of query: 531 Effective length of database: 543 Effective search space: 288333 Effective search space used: 288333 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: 53 (25.0 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