Align NADH-dependent phenylglyoxylate dehydrogenase subunit alpha; Phenylglyoxylate:NAD oxidoreductase; Phenylglyoxylate:acceptor oxidoreductase; EC 1.2.1.58 (characterized)
to candidate WP_051302452.1 A3GO_RS0115710 phenylglyoxylate dehydrogenase
Query= SwissProt::Q8L3B1 (417 letters) >NCBI__GCF_000428045.1:WP_051302452.1 Length = 412 Score = 586 bits (1511), Expect = e-172 Identities = 278/409 (67%), Positives = 339/409 (82%), Gaps = 1/409 (0%) Query: 9 AVAAKAPRKQKVILAEGNEAAALGVALARPDMVSVYPITPQSSLVEHVAKLIADGRMDAD 68 A+ K P + I+ +GNEAAA VALARPD+V+VYPITPQSSLVE+V++ IADG++ A+ Sbjct: 5 ALKMKHPGCAQSIVCDGNEAAAWAVALARPDLVAVYPITPQSSLVEYVSQFIADGKIQAE 64 Query: 69 IVDAEGEHSVLSVLQGGALAGARTYTATCGPGLAFMFEPYFRTSGMRLPIVLTIVTRDGI 128 +++ EGEHSVLS L G ALAG RTYTATCGPGLAFMFEPY+RT GMRLPIV ++VTRDGI Sbjct: 65 LMNVEGEHSVLSALHGAALAGGRTYTATCGPGLAFMFEPYWRTPGMRLPIVASLVTRDGI 124 Query: 129 TPQSVWGGHQDAMTVREAGWIQVYCESVQEVLDTTVMAFKIAEHHDVMLPVNVCLDGNYL 188 TPQ VWGG QDAMT++E GWIQ+YCE+VQEVLDTT+MA++IAEHHDVMLPVN+C DGNYL Sbjct: 125 TPQCVWGGQQDAMTMKETGWIQIYCETVQEVLDTTIMAYRIAEHHDVMLPVNICHDGNYL 184 Query: 189 SYGASRVELPDQAVVDEFMGEKNVNWHVALDPLRPMAVDPLTGGTTGKGPQTFVRYRKGQ 248 SYG ++V++P+Q+ VD+++GEK+VNWHVALDP+RPMAVDPLTGG G GP FV YRKG Sbjct: 185 SYGVTQVDVPEQSAVDDYLGEKDVNWHVALDPMRPMAVDPLTGGAGGPGPSKFVAYRKGL 244 Query: 249 CRGMQNALSVIEEVHADWAKRIGRSFAPLVEEYRLDDAEFAIMTLGSMTGAAKDAVDEAR 308 C GMQNAL VIE+ HADWA GR +APLVEEYRLDDA++A++T+GSMTGAAKDA+D AR Sbjct: 245 CEGMQNALGVIEQAHADWADIFGRDYAPLVEEYRLDDADYALVTIGSMTGAAKDAIDSAR 304 Query: 309 EAGKKIGLIKIKTFSPFPVEALKKALGKVKALGVIDRSVGFRWNCGPMYQETLGVLYRLG 368 G+++GLIKIKTF PFPVEA+ +AL KV+A+GV+DRSV + W+CGP+YQE L LYR G Sbjct: 305 LRGERVGLIKIKTFRPFPVEAMTRALKKVEAVGVVDRSVHYGWDCGPLYQEVLSCLYRAG 364 Query: 369 RHIPSISYIGGLAGADITIPHVHRVIDETEALLNGAVAPTEPVWLNEKD 417 + + S S+IGGLAGAD+T H R I+ T LL G PVWLNE D Sbjct: 365 KPVASGSFIGGLAGADLTEGHFARAIERTAQLLAGTEF-DGPVWLNEND 412 Lambda K H 0.319 0.135 0.403 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: 582 Number of extensions: 12 Number of successful extensions: 2 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: 417 Length of database: 412 Length adjustment: 31 Effective length of query: 386 Effective length of database: 381 Effective search space: 147066 Effective search space used: 147066 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: 50 (23.9 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