Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate WP_034273599.1 AMYHA_RS20335 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-15108 (486 letters) >NCBI__GCF_000504245.1:WP_034273599.1 Length = 496 Score = 382 bits (980), Expect = e-110 Identities = 211/477 (44%), Positives = 291/477 (61%), Gaps = 13/477 (2%) Query: 14 FIDGKFVPSLDGKTFDNI-NPATEEKLGTVAEGGAAEIDLAVQAAKKALN-GPWKKMTAN 71 FIDG++V + + NPA +L TV E ++D AV AA++A + PW+ TA Sbjct: 5 FIDGRWVDTTGTAPARVVLNPANAAELATVCEADEKDVDAAVAAARRAFDDSPWRATTAR 64 Query: 72 ERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNE 131 ER +LR++ L+ KE L+ ESLDTGK T G +D+ F + Y NE Sbjct: 65 ERGELLREIARLLQRDKEHLARTESLDTGK-TMAEGRVDVDDVTSVFRY---YANLADNE 120 Query: 132 ATQMDDVA----LNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTP 187 A ++ D ++ + PVGV LI PWN PLL M+WKLAPALAAGNTVVMKP+E+TP Sbjct: 121 AGRVVDTGDASVISRVVHEPVGVCSLIAPWNYPLLQMSWKLAPALAAGNTVVMKPSEVTP 180 Query: 188 MTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASA 247 +T L + +AGVP GVVNLV G G N GA + HPDV+ +SFTG TGK IMA A Sbjct: 181 LTTIELMRLVEEAGVPAGVVNLVLGGGAN-VGAPMVSHPDVDLVSFTGGLETGKKIMAMA 239 Query: 248 AKTLKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAF 307 A+ +KR++ ELGGKNPNV+FAD++ D ++ + ++F + G+VC GSR+ VE ++ F Sbjct: 240 AEGVKRVALELGGKNPNVVFADADFDTAVDYALMAAFAHSGQVCSAGSRLIVESDIHDEF 299 Query: 308 LEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRP--EG 365 + + + + +GD D T+ G L S EH ++V +I+ A EG ++ GG RP Sbjct: 300 VAELARRADAIRLGDGLDPATECGPLSSAEHRDKVERHIEEAKTEGARLVVGGHRPTEPE 359 Query: 366 LEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTN 425 L GYFL PT+ R+ R+V++E+FGPVVTV FDTE+E + NDT YGL+ +VWT+ Sbjct: 360 LADGYFLRPTVFADCDREMRIVQDEVFGPVVTVERFDTEDEAIRLANDTEYGLAGAVWTS 419 Query: 426 DLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNI 482 D RA RVAG + G VW+N + + +GG +SGIGRE G E Y E +I Sbjct: 420 DASRAQRVAGALRHGTVWINDFHPYLPQAEWGGFGKSGIGRELGPSGLEEYRETKHI 476 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: 630 Number of extensions: 26 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: 496 Length adjustment: 34 Effective length of query: 452 Effective length of database: 462 Effective search space: 208824 Effective search space used: 208824 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