Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate WP_051061199.1 R2APBS1_RS05730 2-hydroxymuconic semialdehyde dehydrogenase
Query= BRENDA::Q8BH00 (487 letters) >NCBI__GCF_000230695.2:WP_051061199.1 Length = 487 Score = 478 bits (1231), Expect = e-139 Identities = 237/471 (50%), Positives = 328/471 (69%), Gaps = 7/471 (1%) Query: 22 NSYIDSYDPSTGEVYCKVPNSGKEEIEAAVEAAREAFPAWSSRSPQERSLVLNRLADVLE 81 ++++D +DP+TG+V+ P+S ++ AAV+AAR A P W+ ++R+ LNRLAD++E Sbjct: 12 DAWLDVHDPATGQVFMHCPDSSTADVAAAVDAARRAAPGWAGTPIEQRAHYLNRLADLVE 71 Query: 82 QSLEELAQAESKDQGKTLTLARTMDIPRSVLNFRFFASSNLHHVSECTQM----SHLGCM 137 LEE A ES+D GK L LAR +DIPR+V N R+FA++ + SE M S +G + Sbjct: 72 ARLEEFAALESRDSGKPLGLARRLDIPRAVSNLRYFAAAIVGWGSESHAMEAGASGIGAI 131 Query: 138 HYTVRTPVGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVTAWMFCKLLDKA 197 +YT+R P+G+ G ISPWNLPLYL +WKIAPA+AAG+TV+AKPSE+T TA + +L +A Sbjct: 132 NYTLRQPLGVVGCISPWNLPLYLFSWKIAPALAAGSTVVAKPSEVTPCTAALLGELSIQA 191 Query: 198 GVPPGVINIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAPHCKKLSLELGGK 257 G PPGV+NIV G GP VGEA+V HP V +SFTGS T RI ++A KK+SLE+GGK Sbjct: 192 GFPPGVLNIVQGRGPSVGEAIVEHPAVKAVSFTGSTATGARIAAIAAAQFKKVSLEMGGK 251 Query: 258 NPAIIFEDANLEEC-IPATVRSSFANQGEICLCTSRIFVQRSIYSEFLKRFVEATRKWKV 316 NPAI+F DA L + + VRS FANQGEICLC SR+ VQRSIY F +R++ + +V Sbjct: 252 NPAIVFADAELSDANLDTIVRSGFANQGEICLCGSRLLVQRSIYDAFRQRYLARVQALRV 311 Query: 317 GVPSDPSANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLPLRNQAGYFMLPT 376 G P+D +++GA++S+AH +KV + +A+ EG R+LCG G LSLP R G+F+ PT Sbjct: 312 GDPNDAGSDLGAMVSQAHYDKVLGCIEQARAEGGRVLCGGGA--LSLPGRCAGGWFIAPT 369 Query: 377 VITDIKDESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVWSKDVGRIHRVAK 436 V + + +EIFGPV ++PF+ E E + AN RYGLAA++W++D+ R HR+A Sbjct: 370 VFEGLPSAAPTNQQEIFGPVVSLIPFEDEAEALAIANDSRYGLAASLWTQDLARAHRLAA 429 Query: 437 KLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTITIKY 487 L+ G+VW NCWL+R+L PFGG+K SG+GREG ++ FFTE K I + Y Sbjct: 430 LLEFGIVWINCWLLRDLRTPFGGVKQSGLGREGGSEALHFFTEPKNICLAY 480 Lambda K H 0.319 0.134 0.404 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: 596 Number of extensions: 25 Number of successful extensions: 4 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: 487 Length of database: 487 Length adjustment: 34 Effective length of query: 453 Effective length of database: 453 Effective search space: 205209 Effective search space used: 205209 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: 52 (24.6 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