Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate GFF2231 Psest_2276 NAD-dependent aldehyde dehydrogenases
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__psRCH2:GFF2231 Length = 506 Score = 346 bits (888), Expect = e-100 Identities = 194/480 (40%), Positives = 276/480 (57%), Gaps = 12/480 (2%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 ++I G+FVP + G+ F N +P E + GA +I+ A+ AA A + W K + + Sbjct: 21 NYIGGEFVPPVKGEYFVNTSPVNGEVIAEFPRSGAEDIEKALDAAHAAADA-WGKTSVQD 79 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R +L K+ D I E+L+V E+ D GK + + D+P AA +F +F+ IR A Sbjct: 80 RALILLKIADRIEANLEKLAVAETWDNGKAVRETLNADVPLAADHFRYFAGCIRAQEGSA 139 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 ++++ Y P+GV+G I PWN PLL+ WKLAPALAAGN +V+KPAE TP++ V Sbjct: 140 AEINEHTAAYHFHEPLGVVGQIIPWNFPLLMAAWKLAPALAAGNCIVLKPAEQTPLSIMV 199 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 E+ D +P GV+N+V GFG AG AL + I+FTG T G IM AA+ + Sbjct: 200 FIEVVGDL-LPPGVLNIVQGFG-REAGQALATSTRIAKIAFTGSTPVGSHIMRCAAENII 257 Query: 253 RLSYELGGKNPNVIFADSNLDE--VIETTMKS---SFINQGEVCLCGSRIYVERPAYEAF 307 + ELGGK+PN+ F D E IE + +F NQGEVC C SR ++ +E F Sbjct: 258 PSTVELGGKSPNIFFEDIMNAEPAFIEKAAEGLVLAFFNQGEVCTCPSRALIQESIFEPF 317 Query: 308 LEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGG---KRPE 364 +E + K K + G+P D T VGA S++ ++++ Y+++A +EG ILTGG K Sbjct: 318 MEVVMKKIKAIKRGNPLDTDTMVGAQASEQQFDKILSYMEIAQQEGAQILTGGAAEKLEG 377 Query: 365 GLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWT 424 L GY+++PT+I G + RV +EEIFGPVV V F E E L NDT +GL A VWT Sbjct: 378 SLSTGYYVQPTLIKGHNK-MRVFQEEIFGPVVGVATFKDEAEALAIANDTEFGLGAGVWT 436 Query: 425 NDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICI 484 D+ RA+R+ I+AG VW N + L FGG K+SG+GRE + Y + N+ I Sbjct: 437 RDINRAYRMGRGIKAGRVWTNCYHLYPAHAAFGGYKKSGVGRETHKMMLDHYQQTKNLLI 496 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: 606 Number of extensions: 26 Number of successful extensions: 6 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: 506 Length adjustment: 34 Effective length of query: 452 Effective length of database: 472 Effective search space: 213344 Effective search space used: 213344 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 17 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