Align periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13) (characterized)
to candidate Echvi_1847 Echvi_1847 Choline dehydrogenase and related flavoproteins
Query= reanno::Pedo557:CA265_RS15345 (567 letters) >FitnessBrowser__Cola:Echvi_1847 Length = 559 Score = 721 bits (1862), Expect = 0.0 Identities = 337/558 (60%), Positives = 421/558 (75%) Query: 10 AENTYDAIVIGSGISGGWAAKELTEKGLRVLMLERGMNIEHITGYETAMKNPWDFKHAGK 69 A YDAIV+GSGISGGWAAKELTEKGL+VL+LERG N+EH+ Y+ A PW+ H G+ Sbjct: 2 ANQEYDAIVVGSGISGGWAAKELTEKGLKVLLLERGQNVEHVKDYKNATLPPWEIPHRGR 61 Query: 70 LTEEQKRTHPVQKRDYPYQEANEKWWVNDLECPYTEDKRFDWYRGFHVGGKSLMWGRQSY 129 T E HP KRDY E WW ++ PY E+K F W+RG+ VGG+SL+WGRQSY Sbjct: 62 RTTEMVENHPNLKRDYVLNELVLDWWAHEDTSPYVEEKPFTWFRGYQVGGRSLLWGRQSY 121 Query: 130 RLSDHNFEDNARDGHGSDWPVRYAELSPWYDYAERFAGISGSKENWPTCPDGQFLPPMDL 189 R SD +FE N ++G DWP+RY +++PWYDY E+FAGI+G+++ PDG+F+PP + Sbjct: 122 RWSDLDFEANLKEGIAVDWPIRYKDIAPWYDYVEKFAGIAGNRDGLDVLPDGEFMPPFAM 181 Query: 190 NIVEKSVKARIEEHYKRERIMMIGRVANLTVPHKGRGNCQYRNLCSRGCPFGAYFSTQSS 249 N VEK VK RI +H++ +R ++ RVAN+T P GR CQ RN C GCPFG YFSTQ+S Sbjct: 182 NCVEKDVKERIAKHFEGKRHLINSRVANITEPLPGRPGCQARNKCWLGCPFGGYFSTQAS 241 Query: 250 TLPAAMATKRLTLRPYSIVNHIIYDKDTKKAKGVMVIDAETNKTMEFYAKIVFVNGSTLG 309 TLPAAMAT LTLRPYSIV+ ++YDKDTKKA GV ++DAET +T+E+ +KIVF+ S L Sbjct: 242 TLPAAMATGNLTLRPYSIVHRVLYDKDTKKATGVEIVDAETMETIEYKSKIVFLCASALN 301 Query: 310 STFVLLNSTSEAHPNGLGNGSGQLGHNLMDHHFRCGASGEAEGFDDKYTYGRRANGIYIP 369 S VL+ S ++ P GLG+ SG+LGHN+MDHHFR GASG EG+DDKY +GRR GIYIP Sbjct: 302 SAHVLMRSATDIWPEGLGSSSGELGHNVMDHHFRLGASGTVEGYDDKYYFGRRPGGIYIP 361 Query: 370 RYQNIGNDKRDYLRGFGYQGGASRANWQGDVAELSFGADLKQKMTTPGKWSMGLGGFGEM 429 RY+N+G+DKRDY+RGFGYQGGASR+ W DVAE++ G +K+ +T PG WSMG+ FGE+ Sbjct: 362 RYRNVGDDKRDYVRGFGYQGGASRSGWGRDVAEMNIGGPMKEALTEPGPWSMGMMAFGEI 421 Query: 430 LPYYENKVYIDKTKKDKWGQPVLAIDCEYKENEKKMRVDMMNDAAEMLEKAGMKNIKTFD 489 LPY+EN + I K KDKWG L ++ E K+NE+KMR DMMNDAAEMLE AG+KNI T+D Sbjct: 422 LPYHENTIKISKDVKDKWGMYALVMNAEIKDNEQKMRKDMMNDAAEMLEAAGVKNIHTYD 481 Query: 490 NGCYPGMAIHEMGTARMGNDPKTSVLNKWNQMHEVNNVFVTDGSCMPSIACQNPSLTFMA 549 +G G IHEMGTARMG DPKTSVLN+ NQ+ + NVFVTDG+ M S A NPSLT+MA Sbjct: 482 SGYTFGQGIHEMGTARMGRDPKTSVLNENNQVWDAKNVFVTDGAAMTSAAAVNPSLTYMA 541 Query: 550 LTARACDYAVKELKKKNI 567 LTARA D+AVKELKK N+ Sbjct: 542 LTARAADFAVKELKKGNL 559 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: 1066 Number of extensions: 44 Number of successful extensions: 1 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: 559 Length adjustment: 36 Effective length of query: 531 Effective length of database: 523 Effective search space: 277713 Effective search space used: 277713 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