Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate WP_045585596.1 AL072_RS27435 aldehyde dehydrogenase family protein
Query= BRENDA::Q83XU8 (485 letters) >NCBI__GCF_001305595.1:WP_045585596.1 Length = 484 Score = 294 bits (753), Expect = 4e-84 Identities = 173/457 (37%), Positives = 251/457 (54%), Gaps = 17/457 (3%) Query: 25 PLNNAVIAKVHEAGRAEVDAAVAAAQAALKGAWGRMSLAQRVEVLYAVADGINRRFDDFL 84 P A + A+VD AVAAA+AA A+ S +R+ ++ + D R+D Sbjct: 35 PATEEPFATIALGTSADVDRAVAAARAAFP-AFSATSREERLALMRRLLDAYKARYDAVA 93 Query: 85 AAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRPV 144 + G P +LA G A+ + +++ E T + P+ Sbjct: 94 DTLSREMGAPTTLAHRSQAAMGTAHLARMIETLESFAFEELRGST--------LISKEPI 145 Query: 145 GVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVYN 204 GVVG+I PWN P+ + KV PALA G T+V+KPSE P A L E ++ AGVP GV+N Sbjct: 146 GVVGMITPWNWPINQIMCKVAPALAAGCTMVLKPSEIAPLNATLFAEAVHEAGVPKGVFN 205 Query: 205 VVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADGARPVSLELGGKNAAIVFA 264 +V+G GP + GE + HP V+ ++FTG T G + KAAAD + V ELGGK+A I+ Sbjct: 206 LVNGDGP-TVGEAIARHPGVDMVSFTGSTRAGILVAKAAADTVKRVHQELGGKSANIILD 264 Query: 265 DCDLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPEDLAT 324 D DLD+A++ + SC N GQ C R++V + D+ ++ + AE ++ G P T Sbjct: 265 DADLDRAVKLGVESCMNNSGQSCNAPTRMFVPASLHDQAIAIARTTAERLKAGAPAAADT 324 Query: 325 GMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGDDSV 384 +GP++SQ +K+ + + GA +VTGG P PE L G +V+PT++ + DD Sbjct: 325 RLGPVVSQIQYDKIQRLIEAGIAEGAELVTGG--PGRPEGLNRGYYVRPTVFANVTDDMT 382 Query: 385 VAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIAWVN 444 +AREEIFGP ++P+ SEEE IRRAND YGLA + + +L RA +VA + G ++N Sbjct: 383 IAREEIFGPVLAILPYGSEEEAIRRANDTPYGLASYVQSGSLERARKVAARMRSGNVYIN 442 Query: 445 --SWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELK 479 +W D FGG KQSG GRE LE + E+K Sbjct: 443 HPAW---DAGAPFGGYKQSGNGREYAEFGLEEFLEIK 476 Lambda K H 0.318 0.135 0.406 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: 518 Number of extensions: 19 Number of successful extensions: 5 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: 485 Length of database: 484 Length adjustment: 34 Effective length of query: 451 Effective length of database: 450 Effective search space: 202950 Effective search space used: 202950 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 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