Align NADH-dependent phenylglyoxylate dehydrogenase subunit beta; Phenylglyoxylate:NAD oxidoreductase; Phenylglyoxylate:acceptor oxidoreductase; EC 1.2.1.58 (characterized)
to candidate WP_011384089.1 AMB_RS08495 hypothetical protein
Query= SwissProt::Q8L3A9 (446 letters) >NCBI__GCF_000009985.1:WP_011384089.1 Length = 469 Score = 600 bits (1546), Expect = e-176 Identities = 280/440 (63%), Positives = 345/440 (78%), Gaps = 8/440 (1%) Query: 1 MGRAYSTIAFDPAKCDGCGDCMTACAQAKTGTDDIARSRIQIYGREGAADKTFELALCRQ 60 MG A+ +I+F + CDGCGDCMTAC+QAK G SRI I GA +FE ALCRQ Sbjct: 1 MGVAFDSISFKASLCDGCGDCMTACSQAKGGA-----SRISIV--PGAKAGSFETALCRQ 53 Query: 61 CADPKCVTVCPAGALNKDGTSGVIGWDATKCVDCLLCTVGCAYAGIALDEATGHVAKCDT 120 C DPKCV VCP+GAL+KDG +G+IGWDA+KCVDCLLCT GCAY GIA+DE+ V KCD Sbjct: 54 CGDPKCVQVCPSGALDKDGGNGIIGWDASKCVDCLLCTAGCAYGGIAVDESVARVGKCDQ 113 Query: 121 CDGNPACVPACPHGALKHITTANIYNEVGDWEDLFAPGLAGCQGCNTELLMRHTLRRVGP 180 CDG+PACV CP GAL+ +I+NE G EDLF PGL+GCQGCN+EL+MRH +R++G Sbjct: 114 CDGDPACVKVCPTGALEFRKAGSIFNEYGAKEDLFVPGLSGCQGCNSELIMRHAMRKIGR 173 Query: 181 DTVLATPPGCVPGMGSVGFNGTTGTKVPVFHPLLTNTAAMLAGIKRQYKRVGR-DVQALA 239 ++VLATPPGC+PGMGSVG+NG TGTKVPVFHPLLTNTA+ML+GI+R Y R+GR D+ +A Sbjct: 174 NSVLATPPGCIPGMGSVGYNGKTGTKVPVFHPLLTNTASMLSGIRRYYDRIGRKDIVVMA 233 Query: 240 IAGDGGASDVGFQSLSGRAERGEQMLFMVVDNEGYMNTGMQRSSCTPYGAWTSTTPVGET 299 +AGDGG +D GF ++SG AERGE++L++ VDNEGYMNTGMQRS TPYG+WTSTTPVGE Sbjct: 234 LAGDGGTADCGFHAVSGAAERGEKVLYVCVDNEGYMNTGMQRSGTTPYGSWTSTTPVGEH 293 Query: 300 SRGKTQDAKNLPLIMVNHRCAYVATASTAYMEDLYDKLDKAIAASKNGFAYLHVYSPCTT 359 +GKTQDAKNLPLIM H+C YVATAST YMEDLY+KLD+AIAAS GF+YLH+YSPC T Sbjct: 294 MQGKTQDAKNLPLIMTAHKCRYVATASTGYMEDLYEKLDRAIAASFEGFSYLHIYSPCPT 353 Query: 360 AWRFPSNLNMEVARKAVETNFVMLWEYTPQDGLHFTKPVDDPLPVTDYLKAMGRFRHLTP 419 WR PS+ ++ R +V++NF LWEYT GL FT D+ PV+ Y+K +G++RHL+P Sbjct: 354 GWRIPSSKVIDACRLSVDSNFNPLWEYTNTSGLRFTHSPDNAHPVSAYVKMIGKYRHLSP 413 Query: 420 EQVEHIQKKVVENQKFVERM 439 +Q+ HIQ KV E ++ M Sbjct: 414 DQLAHIQAKVDEQVALLKLM 433 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: 895 Number of extensions: 43 Number of successful extensions: 6 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: 469 Length adjustment: 33 Effective length of query: 413 Effective length of database: 436 Effective search space: 180068 Effective search space used: 180068 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 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