Align NADH-dependent phenylglyoxylate dehydrogenase subunit beta; Phenylglyoxylate:NAD oxidoreductase; Phenylglyoxylate:acceptor oxidoreductase; EC 1.2.1.58 (characterized)
to candidate WP_004303011.1 C665_RS06110 thiamine pyrophosphate TPP-binding domain-containing protein
Query= SwissProt::Q8L3A9 (446 letters) >NCBI__GCF_000310185.1:WP_004303011.1 Length = 451 Score = 772 bits (1993), Expect = 0.0 Identities = 366/448 (81%), Positives = 396/448 (88%), Gaps = 5/448 (1%) Query: 1 MGRAYSTIAFDPAKCDGCGDCMTACAQAKTGTDDIARSRIQIYGREGAADKT-----FEL 55 MG+AYSTIAFDPAKCDGCG CMTACA K + D RS IQI GA + FEL Sbjct: 1 MGQAYSTIAFDPAKCDGCGKCMTACASVKFDSTDTTRSLIQIVRSGGARIEPPRPGEFEL 60 Query: 56 ALCRQCADPKCVTVCPAGALNKDGTSGVIGWDATKCVDCLLCTVGCAYAGIALDEATGHV 115 ALCRQCADPKCVTVCPAGAL K+GT+GVI WDA+KCVDCLLCT+GC YAGIALDE +G V Sbjct: 61 ALCRQCADPKCVTVCPAGALGKNGTTGVIDWDASKCVDCLLCTIGCTYAGIALDEHSGRV 120 Query: 116 AKCDTCDGNPACVPACPHGALKHITTANIYNEVGDWEDLFAPGLAGCQGCNTELLMRHTL 175 +KCDTC+G PACVPACP GAL+HITTA IYNEVG WEDLFAPGLAGCQGCNTELLMRH L Sbjct: 121 SKCDTCEGKPACVPACPTGALRHITTARIYNEVGSWEDLFAPGLAGCQGCNTELLMRHAL 180 Query: 176 RRVGPDTVLATPPGCVPGMGSVGFNGTTGTKVPVFHPLLTNTAAMLAGIKRQYKRVGRDV 235 RRVGPDTVLATPPGCVPGMGSVGFNGTTGTKVPVFHPLLTNTA+MLAG+KRQY+RVGR V Sbjct: 181 RRVGPDTVLATPPGCVPGMGSVGFNGTTGTKVPVFHPLLTNTASMLAGVKRQYERVGRKV 240 Query: 236 QALAIAGDGGASDVGFQSLSGRAERGEQMLFMVVDNEGYMNTGMQRSSCTPYGAWTSTTP 295 A+AIAGDGGASDVGFQSLSG AERGE++LFMVVDNEGYMNTGMQRSSCTPYGAWTSTTP Sbjct: 241 TAMAIAGDGGASDVGFQSLSGAAERGERILFMVVDNEGYMNTGMQRSSCTPYGAWTSTTP 300 Query: 296 VGETSRGKTQDAKNLPLIMVNHRCAYVATASTAYMEDLYDKLDKAIAASKNGFAYLHVYS 355 +G RGKTQDAKNLP+IMVNHRC YVATASTAYMEDLY+KLDKA+AAS+ GFAYLHVYS Sbjct: 301 IGAHGRGKTQDAKNLPMIMVNHRCEYVATASTAYMEDLYEKLDKALAASERGFAYLHVYS 360 Query: 356 PCTTAWRFPSNLNMEVARKAVETNFVMLWEYTPQDGLHFTKPVDDPLPVTDYLKAMGRFR 415 PCTT WRF S LN+EVARKAVE+NFV LWEYTP+ GLHFT+PVD PLPV DYLKAMGRFR Sbjct: 361 PCTTGWRFQSALNIEVARKAVESNFVTLWEYTPEAGLHFTRPVDKPLPVADYLKAMGRFR 420 Query: 416 HLTPEQVEHIQKKVVENQKFVERMTEHA 443 HL+PEQVEHIQ KV EN +FV ++ E A Sbjct: 421 HLSPEQVEHIQNKVAENLRFVRKIAEQA 448 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: 919 Number of extensions: 46 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: 446 Length of database: 451 Length adjustment: 33 Effective length of query: 413 Effective length of database: 418 Effective search space: 172634 Effective search space used: 172634 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 Sep 24 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