Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_023433101.1 N177_RS14415 aldehyde dehydrogenase
Query= BRENDA::Q1XGK8 (486 letters) >NCBI__GCF_000496075.1:WP_023433101.1 Length = 492 Score = 287 bits (735), Expect = 5e-82 Identities = 174/484 (35%), Positives = 256/484 (52%), Gaps = 12/484 (2%) Query: 5 KHFINGAFVGSASGRTFEDINPSNGQVIGHVHEAGRAEVDAAVKAARAALKGP-WGKLSV 63 +++I+GAF +G +FE ++P+ G+ ++ A A+VD AV+AA A P W +L+ Sbjct: 7 RNYIDGAFCEGGAG-SFESVDPATGEAWANMPAANAADVDRAVRAADRAFHDPSWSRLTA 65 Query: 64 AERAEILHRVADGITARFDEFLEAECLDTGKPKSLASHIDIPRGAANFKVFADLLKNVAN 123 +R ++L+R+AD + E E DTGK S I A ++ +A L + Sbjct: 66 TQRGKLLYRLADLVAENAQALAELETRDTGKIIRETS-AQIAYVADYYRYYAGLADKIEG 124 Query: 124 EAFEMATPDGAGAINYAVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNTVVVKPSEET 183 + PD Y R P GV+ + PWN L L K+GPALA G TVV+K SE+ Sbjct: 125 AHLPIDKPDME---TYLRREPIGVVAAVVPWNSQLFLSAVKLGPALAAGCTVVLKASEDG 181 Query: 184 PLTATLLGEVMQAAGVPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGEVIMRA 243 P ++ AG P GV N++ GFG D G+ L HP V FTG T I+R Sbjct: 182 PAPLLAFARLVDQAGFPPGVVNILTGFG-DQCGSALASHPLVARIAFTGGPATARHIVRH 240 Query: 244 AAKGVRQVSLELGGKNAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDE 303 +A+ + V+LELGGK+ +VF D D+D + FA GQ C+ R+ V+R I D Sbjct: 241 SAENLAAVTLELGGKSPVVVFEDADLDSVANAVVAGIFAATGQSCVAGSRLIVQRGIKDA 300 Query: 304 FVARLKAGAESLMIGPPDDASSNFGPLVSLKHREKVLSYYQQAVDDGGSVITGGGVPD-M 362 + RL A ++ IG P + GPL + + + +++ GG ++TGGG PD Sbjct: 301 LLERLVQKARAIRIGDPQAQETEMGPLATARQLRHIEDVIARSLAAGGRLVTGGGRPDGF 360 Query: 363 PAHLAGGAWVQPTIWTGLSDDSAVVTEEIFGPCCHIRPFDTEEEAIELANSLPYGLASAI 422 PA G + +PTI + V EE+FGP + F+ E EA+E AN PYGLAS + Sbjct: 361 PA----GHYFEPTIIDCDATTIPSVEEELFGPVLSVLGFEEETEAVEFANRTPYGLASGV 416 Query: 423 WTENGSRAHRVAGQIEAGIVWVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNI 482 +T + +RAHR+ I AG+VWVN++ FGG SG GREGG+ + YT K + Sbjct: 417 FTASLTRAHRMIRAIRAGVVWVNTYRAVSPIMPFGGYGLSGSGREGGLDAALDYTRTKAV 476 Query: 483 CVKL 486 +++ Sbjct: 477 WIRV 480 Lambda K H 0.318 0.136 0.411 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: 666 Number of extensions: 30 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: 486 Length of database: 492 Length adjustment: 34 Effective length of query: 452 Effective length of database: 458 Effective search space: 207016 Effective search space used: 207016 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