Align 2-aminomuconic semialdehyde dehydrogenase; Aldehyde dehydrogenase 12; Aldehyde dehydrogenase family 8 member A1; EC 1.2.1.32 (characterized)
to candidate WP_028489491.1 Q394_RS0111975 2-hydroxymuconic semialdehyde dehydrogenase
Query= SwissProt::Q9H2A2 (487 letters) >NCBI__GCF_000621325.1:WP_028489491.1 Length = 486 Score = 409 bits (1052), Expect = e-119 Identities = 213/484 (44%), Positives = 304/484 (62%), Gaps = 9/484 (1%) Query: 10 LENFIDGKFLPCSS--YIDSYDPSTGEVYCRVPNSGKDEIEAAVKAAREAFPS-WSSRSP 66 +++FI+G+F+ +S + +P+T + V +GK E++ AV AA A W Sbjct: 4 IKHFINGEFVGSASGKTFANINPATNQQLGIVHEAGKAEVDQAVAAANAALKGPWGKMPV 63 Query: 67 QERSRVLNQVADLLEQSLEEFAQAESKDQGKTLALARTMDIPRSVQNFRFFASSSLHHTS 126 ER +L++VAD + +EF +AE D GK +LA +DIPR NF+ FA + + Sbjct: 64 AERMAILHKVADGINARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLFKNVPT 123 Query: 127 ECTQMDH---LGCMHYTVRAPVGVAGLISPWNLPLYLLTWKIAPAMAAGNTVIAKPSELT 183 E +D G ++Y +R P GV +ISPWNLPL L+TWK+ PA+A GNTV+ KPSE T Sbjct: 124 ESFMLDTPDGKGALNYAIRKPKGVIAVISPWNLPLLLMTWKVGPALACGNTVVVKPSEET 183 Query: 184 SVTAWMLCKLLDKAGVPPGVVNIVFGTGPR-VGEALVSHPEVPLISFTGSQPTAERITQL 242 T +L ++++ AGVP GV N++ G GP GE L +HP++ I+FTG T I + Sbjct: 184 PRTTTLLGEVMNAAGVPKGVYNVIHGFGPNSAGEFLTTHPDINGITFTGETRTGAAIVKA 243 Query: 243 SAPHCKKLSLELGGKNPAIIFEDANLDECIPATVRSSFANQGEICLCTSRIFVQKSIYSE 302 SA H + +S ELGGKNPA++F D ++D+ I T+RS FAN G++CL T R++V++ I++E Sbjct: 244 SADHIRHVSFELGGKNPAVVFADCDMDKAIEGTLRSVFANCGQVCLGTERVYVERPIFNE 303 Query: 303 FLKRFVEATRKWKVGIPSDPLVSIGALISKAHLEKVRSYVKRALAEGAQIWCGEGVDKLS 362 FL R EA ++G D S+G LISK H +KV SY +A+ EGA + G GV ++ Sbjct: 304 FLSRLTEAAEGMQLGAWDDACTSMGPLISKEHQQKVLSYYAKAIEEGANLITGGGVPEM- 362 Query: 363 LPARNQAGYFMLPTVITDIKDESCCMTEEIFGPVTCVVPFDSEEEVIERANNVKYGLAAT 422 P G ++ PT+ T + + + + EEIFGP V PFDSE+EV+ AN+ KYGLAA Sbjct: 363 -PGALAEGNWVQPTIWTGLPETATVVKEEIFGPCCHVQPFDSEDEVVAWANDTKYGLAAA 421 Query: 423 VWSSNVGRVHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKT 482 VW+ N R HRVA +L +G+VW N W +R+L PFGGMK SGIGREG S +F+TE+K Sbjct: 422 VWTENTSRAHRVAAQLDAGIVWVNSWFLRDLRTPFGGMKHSGIGREGGVHSLEFYTELKN 481 Query: 483 ITVK 486 + VK Sbjct: 482 VCVK 485 Lambda K H 0.319 0.133 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: 618 Number of extensions: 22 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: 487 Length of database: 486 Length adjustment: 34 Effective length of query: 453 Effective length of database: 452 Effective search space: 204756 Effective search space used: 204756 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