Align NADH-dependent phenylglyoxylate dehydrogenase subunit beta; Phenylglyoxylate:NAD oxidoreductase; Phenylglyoxylate:acceptor oxidoreductase; EC 1.2.1.58 (characterized)
to candidate WP_041098408.1 SUTH_RS08095 thiamine pyrophosphate-dependent enzyme
Query= SwissProt::Q8L3A9 (446 letters) >NCBI__GCF_000828635.1:WP_041098408.1 Length = 447 Score = 793 bits (2048), Expect = 0.0 Identities = 381/444 (85%), Positives = 399/444 (89%), Gaps = 8/444 (1%) Query: 1 MGRAYSTIAFDPAKCDGCGDCMTACAQAKTGTDDIARSRIQIYGREGAADKTFELALCRQ 60 M RAY+TIAFD AKCDGCGDCMTACA AK G D ARSRIQI G +AD FELALCRQ Sbjct: 1 MTRAYNTIAFDAAKCDGCGDCMTACATAKVGVGDTARSRIQIVG---SADDGFELALCRQ 57 Query: 61 CADPKCVTVCPAGALNKDGTSGVIGWDATKCVDCLLCTVGCAYAGIALDEATGHVAKCDT 120 C DPKCVTVCPAGAL KDG SGVI WD KCVDCLLCTVGCAYAGIALD TGHVAKCDT Sbjct: 58 CGDPKCVTVCPAGALTKDGLSGVIAWDGAKCVDCLLCTVGCAYAGIALDAGTGHVAKCDT 117 Query: 121 CDGNPACVPACPHGALKHITTANIYNEVGDWEDLFAPGLAGCQGCNTELLMRHTLRRVGP 180 CDG PACVPACPH AL ++TT+ IYNEVGDWEDLFAPGLAGCQGCNTELLMRHTLRRVGP Sbjct: 118 CDGAPACVPACPHEALTYVTTSRIYNEVGDWEDLFAPGLAGCQGCNTELLMRHTLRRVGP 177 Query: 181 DTVLATPPGCVPGMGSVGFNGTTGTKVPVFHPLLTNTAAMLAGIKRQYKRVGRDVQALAI 240 +TVLATPPGCVPGMGSVGFNGTTGTKVPVFHPLLTNTAAMLAGIKRQYKRVGRDV ALAI Sbjct: 178 ETVLATPPGCVPGMGSVGFNGTTGTKVPVFHPLLTNTAAMLAGIKRQYKRVGRDVTALAI 237 Query: 241 AGDGGASDVGFQSLSGRAERGEQMLFMVVDNEGYMNTGMQRSSCTPYGAWTSTTPVGE-- 298 AGDGGASDVGFQSLSG AER EQ+LFMVVDNEGYMNTGMQRSSCTPYGAWTSTTPVG+ Sbjct: 238 AGDGGASDVGFQSLSGAAERNEQILFMVVDNEGYMNTGMQRSSCTPYGAWTSTTPVGQGS 297 Query: 299 ---TSRGKTQDAKNLPLIMVNHRCAYVATASTAYMEDLYDKLDKAIAASKNGFAYLHVYS 355 S+GKTQDAKNLPLIMVNHRC YVATASTAYMEDLY+KLDKAI ASK GFAYLHVYS Sbjct: 298 GGMPSQGKTQDAKNLPLIMVNHRCEYVATASTAYMEDLYEKLDKAIQASKRGFAYLHVYS 357 Query: 356 PCTTAWRFPSNLNMEVARKAVETNFVMLWEYTPQDGLHFTKPVDDPLPVTDYLKAMGRFR 415 PCTT WRFP++ NMEVARKAVETNFVMLWEYTP DGL FT+PVDDPLPVTDYLKAMGRFR Sbjct: 358 PCTTGWRFPTDQNMEVARKAVETNFVMLWEYTPGDGLQFTRPVDDPLPVTDYLKAMGRFR 417 Query: 416 HLTPEQVEHIQKKVVENQKFVERM 439 HL+P+Q+ HIQ KVVEN FV++M Sbjct: 418 HLSPDQISHIQSKVVENLAFVKQM 441 Lambda K H 0.320 0.135 0.429 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: 944 Number of extensions: 47 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: 446 Length of database: 447 Length adjustment: 33 Effective length of query: 413 Effective length of database: 414 Effective search space: 170982 Effective search space used: 170982 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 51 (24.3 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