Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_047007132.1 AAW01_RS09770 NAD-dependent succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_001010925.1:WP_047007132.1 Length = 476 Score = 245 bits (626), Expect = 2e-69 Identities = 149/460 (32%), Positives = 242/460 (52%), Gaps = 15/460 (3%) Query: 15 IDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERI 74 I G+ V T + INPATEE LGT+ + ++D A+ AA+ W+ +A++R Sbjct: 11 IAGEKVTGGGRDTEEVINPATEEVLGTLPHATSDDLDRALDAAQSGFR-EWRSTSADKRA 69 Query: 75 AVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSD-----YIRTIT 129 +L +LI ERKE+++ + + GKP G + +A F++ Y RT+ Sbjct: 70 TILTNAANLIRERKEDIAGWLTREQGKPLG-DGRGEAMYSANLLEFYAQEAKRTYGRTLV 128 Query: 130 NEATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMT 189 +V + PVG + PWN P + + K+ ALAAG +V++KP+E TP Sbjct: 129 RGEGSRVEVQYH-----PVGPVAGFAPWNFPAINVMRKIGGALAAGCSVIVKPSEETPAA 183 Query: 190 ATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAK 249 L + DAGVP G V V G P++ L P + ++FTG T GK + AA Sbjct: 184 GIALVQALLDAGVPGGAVQCVFGV-PSNVSEHLLASPIIRKLTFTGSTPVGKHLAKLAAD 242 Query: 250 TLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLE 309 LK + ELGG P ++F D ++D+ ++T + + N G+VC+ R +E +E F + Sbjct: 243 DLKITTMELGGHGPVLVFDDCDVDKAVKTMAGNKYRNAGQVCVSPIRFLIEESIFEQFRD 302 Query: 310 KFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKG 369 FV + +++ VG+ + T +G + + E + I A E G +LTGG+ +G Sbjct: 303 SFVERAEKVRVGNGLEDGTDMGPMANARGRENIQKLIANAKEAGANLLTGGEVIG--NQG 360 Query: 370 YFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRR 429 +F +PT+++ + ++ E FGPV + P E+ ++E+ N YGL+A WT+D R Sbjct: 361 FFHQPTVLSEVPTSADIMNNEPFGPVAILNPMSGEDAMIEEANRLPYGLAAYAWTDDAAR 420 Query: 430 AHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGG 469 R+A ++EAG++ +N + + PFGG+K SG G E G Sbjct: 421 RRRLAAEVEAGMLAINGGSVSTVDAPFGGVKWSGYGSEDG 460 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: 592 Number of extensions: 27 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: 476 Length adjustment: 34 Effective length of query: 452 Effective length of database: 442 Effective search space: 199784 Effective search space used: 199784 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: 51 (24.3 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