Align periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13) (characterized)
to candidate Echvi_1044 Echvi_1044 Choline dehydrogenase and related flavoproteins
Query= reanno::Pedo557:CA265_RS15345 (567 letters) >FitnessBrowser__Cola:Echvi_1044 Length = 566 Score = 523 bits (1346), Expect = e-152 Identities = 262/569 (46%), Positives = 365/569 (64%), Gaps = 15/569 (2%) Query: 1 MMNLNTNLKAENTYDAIVIGSGISGGWAAKELTEKGLRVLMLERGMNIEHITGYETAMKN 60 M NLN K EN++ AIVIGSG+SGG+AAKEL +KG++ L+LERG ++ H Y T Sbjct: 1 MANLNIKGKEENSFGAIVIGSGMSGGFAAKELCDKGVKTLVLERGRSVVHNKDYPTTNMM 60 Query: 61 PWDFKHAGKLTEEQKRTHPVQKRDYPYQEANEKWWVNDLECPYTEDKRFDWYRGFHVGGK 120 PW+F+H G++ E+ +R +PV R Y ++E ++V D E PY ++K FDW RG+ GGK Sbjct: 61 PWEFEHRGQIPEDIQRENPVVSRCYAFREDAAHFFVKDQEHPYIQEKPFDWIRGYQTGGK 120 Query: 121 SLMWGRQSYRLSDHNFEDNARDGHGSDWPVRYAELSPWYDYAERFAGISGSKENWPTCPD 180 SL+W RQ R SDH+FE ARDG DWP+RY +L+PWY Y E+F G++G + P PD Sbjct: 121 SLLWARQVQRWSDHDFEGPARDGFAVDWPIRYKDLAPWYSYVEKFVGVAGFHDGIPHLPD 180 Query: 181 GQFLPPMDLNIVEKSVKARIEEHYKRERIMMIGRVANLT-----VPHKGRGNCQYRNLCS 235 G+FLP ++L E+ K+ +EE Y ++ GR A++T +GRG CQ+R +C Sbjct: 181 GEFLPGIELTAAEEYFKSVVEEKYPGRNVIS-GRYAHITGNAEYYAKQGRGICQHRTICQ 239 Query: 236 RGCPFGAYFSTQSSTLPAAMATKRLTLRPYSIVNHIIYDKDTKKAKGVMVIDAETNKTME 295 RGCPFG YFS+ S++LP A T LTL+ +++V+ IIYD +KA GV VIDA T + E Sbjct: 240 RGCPFGGYFSSNSASLPWAQRTGNLTLKNHAVVHSIIYDDTQQKATGVRVIDANTKEVTE 299 Query: 296 FYAKIVFVNGSTLGSTFVLLNSTSEAHPNGLGNGSGQLGHNLMDHHFRCGASGEAEGFDD 355 +YA I+FVN S L + +LLNSTS+ P+GLGN +G +G + H++R G SGE EG Sbjct: 300 YYAPIIFVNASALNTNLILLNSTSKRFPHGLGNDNGLMGKFIAFHNYRGGVSGEYEGLKS 359 Query: 356 KYTYGRRANGIYIPRYQNIGNDKRDYLRGF--GYQGGASRANWQGDVAELSFGADLKQKM 413 T G+R Y+PR++N+ + +LRG+ G G S+ DV GADL + + Sbjct: 360 FTTEGKRPTSGYMPRFRNVDKQETKFLRGYAAGIHGTRSK-----DVDYSGTGADLVKNI 414 Query: 414 TTP--GKWSMGLGGFGEMLPYYENKVYIDKTKKDKWGQPVLAIDCEYKENEKKMRVDMMN 471 P G W +G GE +P N V +D +KD+W P L ++ +Y +N+ M D Sbjct: 415 MNPSYGPWRIGSHMMGETIPKESNYVALDTAQKDEWDMPQLKVNVDYDQNDLDMIKDYRE 474 Query: 472 DAAEMLEKAGMKNIKTFDNGCYPGMAIHEMGTARMGNDPKTSVLNKWNQMHEVNNVFVTD 531 AEM + AG KNI+T+D+ PG+ IHEMG RMG+DPKTS+LNK +Q+H NV+VTD Sbjct: 475 QLAEMFDAAGFKNIRTWDDERRPGLDIHEMGGVRMGHDPKTSLLNKHHQLHACPNVYVTD 534 Query: 532 GSCMPSIACQNPSLTFMALTARACDYAVK 560 G+CM S + QNPSLT+M ARA D+A+K Sbjct: 535 GACMTSTSTQNPSLTYMVFAARAVDHALK 563 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: 1018 Number of extensions: 50 Number of successful extensions: 3 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: 566 Length adjustment: 36 Effective length of query: 531 Effective length of database: 530 Effective search space: 281430 Effective search space used: 281430 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 Apr 09 2024. 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