Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate AZOBR_RS26825 AZOBR_RS26825 aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__azobra:AZOBR_RS26825 Length = 494 Score = 324 bits (830), Expect = 5e-93 Identities = 178/465 (38%), Positives = 261/465 (56%), Gaps = 7/465 (1%) Query: 12 LHFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTAN 71 L I G+ P+ GKTFD +NPAT + + T A+GG ++D AV+AA A G W +++A Sbjct: 17 LLLIGGELRPAATGKTFDVVNPATGDVIATAADGGERDVDAAVRAAVAA-QGAWARLSAR 75 Query: 72 ERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNE 131 ER +L + G ++ EE+ L +L+TGK ++ A F+ + E Sbjct: 76 ERGRLLVECGRRLVGHAEEIGRLLALETGKAIRTESRVEASLVADTLTFYGGLASELKGE 135 Query: 132 ATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTAT 191 L + R P+GV+G I PWN+PL LM K+APAL AGN V++K AE P+ A Sbjct: 136 TVPFHPKMLTFTQREPIGVVGAIIPWNVPLYLMALKIAPALVAGNAVIVKSAEEAPLAAL 195 Query: 192 VLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTL 251 + ++ +P GV+N++ G GP GA L HP V ++FTG TGKII AA L Sbjct: 196 RVIQVMNQL-LPPGVLNILSGDGPG-CGAPLVTHPGVGKVTFTGSVETGKIISHLAADKL 253 Query: 252 KRLSYELGGKNPNVIFADSNLDEVIETTMKSS-FINQGEVCLCGSRIYVERPAYEAFLEK 310 ++ ELGGK+P ++ D++LD+ I+ + F QG+ C SRI+V ++AF++K Sbjct: 254 IPVTLELGGKSPMIVMGDADLDKAIDGAVAGMRFTRQGQSCTASSRIFVHESLHDAFIDK 313 Query: 311 FVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTIL---TGGKRPEGLE 367 AK + +GDP D T +G +IS + +ERV YI L G I + E L Sbjct: 314 LKAKVDAMTMGDPLDEATDIGTIISPQQFERVQSYIALGETTAGAIAHRCSALPTDERLA 373 Query: 368 KGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDL 427 +G F++P + TGL D R+ +EEIFGPV VI F E+ L ND+ +GL+A++WT DL Sbjct: 374 RGLFVQPVLFTGLANDHRLAREEIFGPVTCVIAFRDYEDALAMANDSDFGLAATIWTRDL 433 Query: 428 RRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHS 472 R A +++AG V VN + +GG KQSG+G+E L + Sbjct: 434 RTALDATRRLQAGFVQVNQNLVVQPGLSYGGFKQSGLGKEASLEA 478 Lambda K H 0.318 0.136 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: 531 Number of extensions: 27 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: 486 Length of database: 494 Length adjustment: 34 Effective length of query: 452 Effective length of database: 460 Effective search space: 207920 Effective search space used: 207920 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 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