Align periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13) (characterized)
to candidate Echvi_1439 Echvi_1439 Choline dehydrogenase and related flavoproteins
Query= reanno::Pedo557:CA265_RS15345 (567 letters) >FitnessBrowser__Cola:Echvi_1439 Length = 566 Score = 733 bits (1893), Expect = 0.0 Identities = 351/569 (61%), Positives = 425/569 (74%), Gaps = 6/569 (1%) Query: 2 MNLNTNLKAENTYDAIVIGSGISGGWAAKELTEKGLRVLMLERGMNIEHITGYETAMKNP 61 MNLN ENTYDAIV+GSGISGGWAAKEL EKGL+ L+LERG N+EHI GY T NP Sbjct: 1 MNLNIKATKENTYDAIVVGSGISGGWAAKELCEKGLKTLVLERGKNVEHIKGYPTTNLNP 60 Query: 62 WDFKHAGKLTEEQKRTHPVQKRDYPYQEANEKWWVNDLECPYTEDKRFDWYRGFHVGGKS 121 W+ H G T E K HP+Q R Y + E +++WVNDLE PY E K F+W RG+HVGG+S Sbjct: 61 WELDHRGWSTNESKEKHPIQSRCYAFGEDTQQFWVNDLENPYNEVKPFNWLRGYHVGGRS 120 Query: 122 LMWGRQSYRLSDHNFEDNARDGHGSDWPVRYAELSPWYDYAERFAGISGSKENWPTCPDG 181 LMWGRQ YRLSD +FE NA+DG+G DWPVRY +L+PWY Y E+FAGISG E P PD Sbjct: 121 LMWGRQCYRLSDIDFEANAKDGYGVDWPVRYKDLAPWYTYVEKFAGISGQAEGLPQLPDS 180 Query: 182 QFLPPMDLNIVEKSVKARIEEHYKRERIMMIGRVANLTVPHKGRGNCQYRNLCSRGCPFG 241 FLP M++N VEK V AR++E + +RI+ IGR A+ T GRG CQYRNLC+RGCPFG Sbjct: 181 HFLPAMEMNCVEKHVAARVKEKFD-DRIITIGRAAHATAALNGRGPCQYRNLCARGCPFG 239 Query: 242 AYFSTQSSTLPAAMATKRLTLRPYSIVNHIIYDKDTKKAKGVMVIDAETNKTMEFYAKIV 301 YFS+ S+TLPAAM T +TLRP+SIV ++YDK+T KA GV ++DAET + E+YAK+V Sbjct: 240 GYFSSNSATLPAAMQTGNMTLRPFSIVTEVLYDKETGKANGVRIMDAETKEYTEYYAKVV 299 Query: 302 FVNGSTLGSTFVLLNSTSEAHPNGLGNGSGQLGHNLMDHHFRCGASGEAEGFDDKYTYGR 361 F+N STLG+ ++LLNS S+A PNGLGNGS Q+GHNLMDHH+ GASG EGF DKY YGR Sbjct: 300 FLNASTLGTAWILLNSVSDAFPNGLGNGSEQVGHNLMDHHYGVGASGAIEGFGDKYYYGR 359 Query: 362 RANGIYIPRYQNI--GNDKRDYLRGFGYQGGASRANWQGDVAELSFGADLKQKMTTPGK- 418 R NGIY+PR++NI ++ DY+RGFGYQGGA R QG A GAD K T P + Sbjct: 360 RPNGIYVPRFRNISEATERPDYVRGFGYQGGAGRGRGQGGPA--GVGADFKLSKTQPSED 417 Query: 419 WSMGLGGFGEMLPYYENKVYIDKTKKDKWGQPVLAIDCEYKENEKKMRVDMMNDAAEMLE 478 WS G+G +GE LPYY+NKV ++ K D +G P L IDCE+KENE MR DM A ++LE Sbjct: 418 WSFGIGSWGEHLPYYDNKVSLNHDKLDAYGLPTLDIDCEFKENEMAMRKDMRQSAVDILE 477 Query: 479 KAGMKNIKTFDNGCYPGMAIHEMGTARMGNDPKTSVLNKWNQMHEVNNVFVTDGSCMPSI 538 G KNI ++D+ PG IHEMGTARMG DPKTSVLN +NQMHEV NV++TDG+ M S Sbjct: 478 AVGAKNINSYDSAPPPGHCIHEMGTARMGKDPKTSVLNGYNQMHEVPNVYITDGAFMASS 537 Query: 539 ACQNPSLTFMALTARACDYAVKELKKKNI 567 ACQNPSLT+MA TARACD+AVKELKK+N+ Sbjct: 538 ACQNPSLTYMAFTARACDHAVKELKKQNL 566 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: 1117 Number of extensions: 51 Number of successful extensions: 4 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 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