Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate AO356_12580 AO356_12580 aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_12580 Length = 497 Score = 366 bits (939), Expect = e-105 Identities = 195/488 (39%), Positives = 291/488 (59%), Gaps = 4/488 (0%) Query: 2 QQTKVKPIDCLHFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKAL 61 Q+ + I+ FI+G++ ++ G+TFD ++P LG +A A+ AV+ A+ Sbjct: 11 QRARDLKIEGRAFINGEYTDAVSGETFDCLSPVDGRLLGKIASCDVADAQRAVENARATF 70 Query: 62 N-GPWKKMTANERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHF 120 N G W ++ ++R + + L+ + EEL++LE+LD GKP S +ID+P AA + Sbjct: 71 NSGVWSRLAPSKRKTTMIRFAGLLKQHAEELALLETLDMGKPISDSLNIDVPGAAQALSW 130 Query: 121 FSDYIRTITNEATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVM 180 + I + +E L R PVGV+G I PWN PL++ WKL PAL+ GN+VV+ Sbjct: 131 SGEAIDKLYDEVAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVVL 190 Query: 181 KPAELTPMTATVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTG 240 KP+E +P+TA +A + +AG+P GV+N++ G+G ++ G AL H DV+ + FTG T Sbjct: 191 KPSEKSPLTAIRIAALAIEAGIPKGVLNVLPGYG-HTVGKALALHMDVDTLVFTGSTKIA 249 Query: 241 KIIMA-SAAKTLKRLSYELGGKNPNVIFADS-NLDEVIETTMKSSFINQGEVCLCGSRIY 298 K +M S +KR+ E GGK+PN++FAD+ +L E+ + NQGEVC GSR+ Sbjct: 250 KQLMIYSGESNMKRIWLEAGGKSPNIVFADAPDLQAAAESAASAIAFNQGEVCTAGSRLL 309 Query: 299 VERPAYEAFLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILT 358 VER + FL + K G+P D T VGAL+ + V YI+ +G ++ Sbjct: 310 VERSIKDTFLPLVIEALKGWKPGNPLDPATNVGALVDTQQMNTVLSYIEAGHSDGAKLVA 369 Query: 359 GGKRPEGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGL 418 GGKR G ++EPTI G++ ++ +EEIFGPV++VI FDT E+ +E NDT YGL Sbjct: 370 GGKRILEETGGTYVEPTIFDGVSNAMKIAQEEIFGPVLSVIAFDTAEQAIEIANDTPYGL 429 Query: 419 SASVWTNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSE 478 +A+VWT D+ +AH A + AG VWVN + D+ PFGG KQSG GR+ LH+F+ Y+E Sbjct: 430 AAAVWTKDISKAHLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTE 489 Query: 479 LTNICIKL 486 L + IKL Sbjct: 490 LKSTWIKL 497 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: 650 Number of extensions: 24 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: 497 Length adjustment: 34 Effective length of query: 452 Effective length of database: 463 Effective search space: 209276 Effective search space used: 209276 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 Apr 09 2024. 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