Align periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13) (characterized)
to candidate N515DRAFT_1321 N515DRAFT_1321 Choline dehydrogenase
Query= reanno::Pedo557:CA265_RS15345 (567 letters) >FitnessBrowser__Dyella79:N515DRAFT_1321 Length = 565 Score = 631 bits (1628), Expect = 0.0 Identities = 304/564 (53%), Positives = 395/564 (70%), Gaps = 9/564 (1%) Query: 11 ENTYDAIVIGSGISGGWAAKELTEKGLRVLMLERGMNIEHITGYETAMKNPWDFKHAGKL 70 ++ YDAIV+G+G+SGGWAAKELTEKGL+ L+L+RG ++H Y TAMK PW+ + + Sbjct: 4 KHVYDAIVVGTGVSGGWAAKELTEKGLKTLVLDRGPMVKH-GDYPTAMKAPWELPYGDEP 62 Query: 71 TEEQKRTHPVQKRD--YPYQEANEKWWVNDLECPYTEDKRFDWYRGFHVGGKSLMWGRQS 128 T HP+ R Y ++ + W+V+D++ PY E + FDW+RG+HVGG+SLMWGRQS Sbjct: 63 TRHDIERHPIHTRPSFYGITQSTKHWFVDDIDNPYEETRPFDWFRGYHVGGRSLMWGRQS 122 Query: 129 YRLSDHNFEDNARDGHGSDWPVRYAELSPWYDYAERFAGISGSKENWPTCPDGQFLPPMD 188 YRLS + E N ++G G DWP+RY +++PWYDY E F G+SGS E+ P PDG FLPPM+ Sbjct: 123 YRLSPMDLEANGKEGVGVDWPIRYDDIAPWYDYVEHFIGVSGSIEHMPQLPDGDFLPPME 182 Query: 189 LNIVEKSVKARIEEHYKRERIMMIGRVANLTVPHKG-----RGNCQYRNLCSRGCPFGAY 243 L VEK + +I + +++ IGR ANL+ P K R CQYRNLC RGCPFGAY Sbjct: 183 LTCVEKDFRDKIAGKFGGRKLI-IGRTANLSAPLKHDKSPQRAPCQYRNLCMRGCPFGAY 241 Query: 244 FSTQSSTLPAAMATKRLTLRPYSIVNHIIYDKDTKKAKGVMVIDAETNKTMEFYAKIVFV 303 FS+ SSTLPAA T +T+ +IV +IYD D KA GV V+DAET E++AK++F+ Sbjct: 242 FSSNSSTLPAAEKTGNMTMVTNAIVYELIYDNDKGKATGVRVLDAETGHQTEYFAKVIFM 301 Query: 304 NGSTLGSTFVLLNSTSEAHPNGLGNGSGQLGHNLMDHHFRCGASGEAEGFDDKYTYGRRA 363 ST GST +LLNSTS PNG GN SG+LGHN+MDH F GA +G+DD+Y GRR Sbjct: 302 CASTFGSTHILLNSTSSRFPNGFGNDSGELGHNIMDHLFGSGARAMVDGYDDRYYSGRRP 361 Query: 364 NGIYIPRYQNIGNDKRDYLRGFGYQGGASRANWQGDVAELSFGADLKQKMTTPGKWSMGL 423 NG YIPRY+N+G+DK +LRG+GYQGGASR +W V G DLK+ TPG WS+ + Sbjct: 362 NGFYIPRYRNVGSDKSSFLRGYGYQGGASRQDWTRLVNTPLIGGDLKRAAQTPGPWSISM 421 Query: 424 GGFGEMLPYYENKVYIDKTKKDKWGQPVLAIDCEYKENEKKMRVDMMNDAAEMLEKAGMK 483 GFGEMLP + NKV +D+ +KDK+G PVL D ++ENE + +++DA EM+ AG + Sbjct: 422 MGFGEMLPSHRNKVTLDRNRKDKYGLPVLNFDAAHEENELAIGKAIVDDALEMMSAAGYR 481 Query: 484 NIKTFDNGCYPGMAIHEMGTARMGNDPKTSVLNKWNQMHEVNNVFVTDGSCMPSIACQNP 543 ++++F G IHEMGTARMG DPKTSVLN WNQMH NV+VTDGS M S CQNP Sbjct: 482 DVRSFKVQANVGAGIHEMGTARMGRDPKTSVLNGWNQMHACKNVYVTDGSFMASSGCQNP 541 Query: 544 SLTFMALTARACDYAVKELKKKNI 567 SLT+MA+TARA +AV+ELK+ NI Sbjct: 542 SLTYMAMTARAASHAVEELKRGNI 565 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: 1071 Number of extensions: 48 Number of successful extensions: 5 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: 565 Length adjustment: 36 Effective length of query: 531 Effective length of database: 529 Effective search space: 280899 Effective search space used: 280899 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