Align NADH-dependent phenylglyoxylate dehydrogenase subunit alpha; Phenylglyoxylate:NAD oxidoreductase; Phenylglyoxylate:acceptor oxidoreductase; EC 1.2.1.58 (characterized)
to candidate WP_011384087.1 AMB_RS08485 hypothetical protein
Query= SwissProt::Q8L3B1 (417 letters) >NCBI__GCF_000009985.1:WP_011384087.1 Length = 405 Score = 560 bits (1443), Expect = e-164 Identities = 267/399 (66%), Positives = 321/399 (80%), Gaps = 1/399 (0%) Query: 19 KVILAEGNEAAALGVALARPDMVSVYPITPQSSLVEHVAKLIADGRMDADIVDAEGEHSV 78 KVI+ +GNEAAA G L+RPDMV+VYPITPQSSLVE++A+ IADGRMDAD++D EGEH+V Sbjct: 8 KVIVCDGNEAAAWGACLSRPDMVAVYPITPQSSLVEYLAQFIADGRMDADLMDVEGEHTV 67 Query: 79 LSVLQGGALAGARTYTATCGPGLAFMFEPYFRTSGMRLPIVLTIVTRDGITPQSVWGGHQ 138 LSVL G LAGARTY+AT GLAFMFEPYFRT G+RLP+V+++VTRD ++P VWGG Q Sbjct: 68 LSVLHGAVLAGARTYSATSAQGLAFMFEPYFRTPGLRLPMVVSLVTRDAVSPTCVWGGQQ 127 Query: 139 DAMTVREAGWIQVYCESVQEVLDTTVMAFKIAEHHDVMLPVNVCLDGNYLSYGASRVELP 198 DAMTV+E GWI +YCE+ QE+LDT +A+K+AEH DVMLPVNV DGNYLSYG +RVELP Sbjct: 128 DAMTVKEVGWIHMYCETQQEILDTIPIAYKVAEHPDVMLPVNVNHDGNYLSYGVARVELP 187 Query: 199 DQAVVDEFMGEKNVNWHVALDPLRPMAVDPLTGGTTGKGPQTFVRYRKGQCRGMQNALSV 258 DQ+VVD F+GEK VNWH LDP RPMAVDPLTGG G GP FV+YRKG C GMQ+AL + Sbjct: 188 DQSVVDAFLGEKQVNWHACLDPERPMAVDPLTGGAGGIGPSLFVKYRKGICAGMQDALRI 247 Query: 259 IEEVHADWAKRIGRSFAPLVEEYRLDDAEFAIMTLGSMTGAAKDAVDEAREAGKKIGLIK 318 IEE H DW +R GR ++PL+EEYR++DAE A++T+GSMTGAAKDAVD+AR +GKKIGL+K Sbjct: 248 IEEAHEDWGRRTGRYWSPLIEEYRMEDAEVALVTIGSMTGAAKDAVDDARASGKKIGLVK 307 Query: 319 IKTFSPFPVEALKKALGKVKALGVIDRSVGFRWNCGPMYQETLGVLYRLGRHIPSISYIG 378 IKTF PFP + +AL +VKA+GV+DRSV F WNCGP+YQE L +Y IP +S+IG Sbjct: 308 IKTFRPFPAARIAQALSRVKAVGVVDRSVNFGWNCGPVYQEVLAAMYAQPVRIPMMSFIG 367 Query: 379 GLAGADITIPHVHRVIDETEALLNGAVAPTEPVWLNEKD 417 GLAGADIT+ H V+ T L G A T PVWLNE D Sbjct: 368 GLAGADITVEHFAEVVHRTFRLAGGEAA-TGPVWLNEND 405 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: 570 Number of extensions: 14 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: 405 Length adjustment: 31 Effective length of query: 386 Effective length of database: 374 Effective search space: 144364 Effective search space used: 144364 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 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