Align periplasmic glucoside 3-dehydrogenase (lacA subunit) (EC 1.1.99.13) (characterized)
to candidate Ga0059261_0546 Ga0059261_0546 Choline dehydrogenase and related flavoproteins
Query= reanno::Cola:Echvi_1847 (559 letters) >FitnessBrowser__Korea:Ga0059261_0546 Length = 560 Score = 498 bits (1282), Expect = e-145 Identities = 262/560 (46%), Positives = 355/560 (63%), Gaps = 12/560 (2%) Query: 2 ANQEYDAIVVGSGISGGWAAKELTEKGLKVLLLERGQNVEHVKDYKNATLPPWEIPHRGR 61 + +DAIV+GSG+SGG+AAKELTEKGL+VL+L+RG VEH +DY P +E+P R Sbjct: 3 STNRFDAIVIGSGVSGGFAAKELTEKGLRVLMLDRGVMVEHGEDYTYDGKPAYEVPARNI 62 Query: 62 RTTEMVENHPNLKRDYVLNELVLDWWAHEDTSPYVEEK--PFTWFRGYQVGGRSLLWGRQ 119 ++E+ + ++ + ++ + +PY ++ F W R VGG+SL+WGR Sbjct: 63 MPKPLIESDYFIAKNGYVAPSNRRFYNDDRLNPYAHDEGSKFFWIRPGAVGGKSLIWGRW 122 Query: 120 SYRWSDLDFEANLKEGIAVDWPIRYKDIAPWYDYVEKFAGIAGNRDGLDVLPDGEFMPPF 179 S+RWS DFEAN +EGI DWPIRY DIAPWY VE + G++G+R+ L LPD EF PP Sbjct: 123 SFRWSADDFEANKREGIDGDWPIRYDDIAPWYSKVENYIGVSGSRENLPQLPDSEFQPPM 182 Query: 180 AMNCVEKDVKERIAKHFEGKRHLINSRVANITEPLP--GRPGCQARNKCWLGCPFGGYFS 237 MN EK VK+R+ F G++ LIN+R++N+TE P R CQ RN+C GC FG YFS Sbjct: 183 PMNIAEKWVKQRLETQFPGRK-LINARLSNLTEDKPEQNRTKCQMRNQCGNGCSFGAYFS 241 Query: 238 TQASTLPAAMATGNLTLRPYSIVHRVLYDKDTKKATGVEIVDAETMETIEYKSKIVFLCA 297 TQA TLPAA ATG LTLR ++V + YD K+ TGV VDA T + + +VFLCA Sbjct: 242 TQAVTLPAARATGRLTLRSDAVVTNLEYDPVRKRVTGVRFVDARTRQAEVVNADLVFLCA 301 Query: 298 SALNSAHVLMRSATDIWPEGLGSSSGELGHNVMDHHFRLGASGTVEGYDDKYYFGRRPGG 357 SA+ S +LM S SSG LG VMDH FR+G G + G + +GRRPGG Sbjct: 302 SAMASTQILMNSRAAGSGRSHFDSSGTLGKYVMDHIFRVGIEGEIPGMSEYIEYGRRPGG 361 Query: 358 IYIPRYRNVG-DDKRDYVRGFGYQGGASRSGWGRDVAE-MNIGGPMKEALTEPGPWSMGM 415 IYIPR+RN+G D+ + RG+GYQGGA R DVA + G MK + + PW + Sbjct: 362 IYIPRFRNIGADENLGFKRGYGYQGGAHR-----DVAPPVGFGASMKHGMRKYAPWKFHI 416 Query: 416 MAFGEILPYHENTIKISKDVKDKWGMYALVMNAEIKDNEQKMRKDMMNDAAEMLEAAGVK 475 AFGE LPY +N++ + D D++G+ + + ++NE +M D ML+AAG+ Sbjct: 417 SAFGECLPYRDNSVSLHADKVDRFGVPLMRFDVRFRENELRMMADARTQGEAMLKAAGLG 476 Query: 476 NIHTYDSGYTFGQGIHEMGTARMGRDPKTSVLNENNQVWDAKNVFVTDGAAMTSAAAVNP 535 ++ +++ + G IHEMG ARMG DP++SVLN +Q DA N++VTDGA M S + VNP Sbjct: 477 SVRSWEGEHVPGDAIHEMGGARMGADPRSSVLNSWSQAHDASNLYVTDGAQMASVSCVNP 536 Query: 536 SLTYMALTARAADFAVKELK 555 SLT+MALT RAAD AV+ L+ Sbjct: 537 SLTFMALTVRAADHAVRTLR 556 Lambda K H 0.317 0.135 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: 857 Number of extensions: 36 Number of successful extensions: 7 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: 559 Length of database: 560 Length adjustment: 36 Effective length of query: 523 Effective length of database: 524 Effective search space: 274052 Effective search space used: 274052 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