Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate GFF3171 PGA1_c32220 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase HpcC
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Phaeo:GFF3171 Length = 503 Score = 386 bits (991), Expect = e-111 Identities = 201/455 (44%), Positives = 284/455 (62%), Gaps = 5/455 (1%) Query: 28 FDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERIAVLRKVGDLILER 87 F I+P + + VA G AA+ID A QAA++A W+ + A +R +L ++ + I R Sbjct: 39 FQTISPVDKSVICDVAHGTAADIDAAAQAARQAF-AEWRDLPAVQRKKILIRIAEGIEAR 97 Query: 88 KEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEATQMDDVALNYAIRRP 147 EE+++ E DTG+ + R A NF +F+D + + +N R P Sbjct: 98 AEEIALCECWDTGQAYKFMSKAAL-RGAENFRYFADQVVQARDGQHLQSPTLMNVTTRVP 156 Query: 148 VGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVLAEICRDAGVPDGVV 207 +G +G+I PWN P +L TWK+APALAAG TVV KPAE +P+TA +L EI +AG+P GV+ Sbjct: 157 IGPVGVITPWNTPFMLSTWKIAPALAAGCTVVHKPAEASPLTARLLVEIAEEAGLPPGVL 216 Query: 208 NLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKRLSYELGGKNPNVIF 267 N V+GFG + AG AL EHP + AI+F GE+ TG +I A TLKR ELGGKNP ++F Sbjct: 217 NTVNGFG-DEAGKALCEHPAIRAIAFVGESRTGSLITKQGADTLKRNHLELGGKNPVIVF 275 Query: 268 ADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVAKTKELVVGDPFDAK 327 D++L+ ++ + + GE C SR+ ++ + F + + + + VG P D Sbjct: 276 EDADLERALDAVIFMIYSINGERCTSSSRLLIQDSIRDDFEARLIERINNIKVGHPLDPT 335 Query: 328 TKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFLEPTIITGLTRDCRVV 387 T++G L+S+EH+ +VT Y +A +EG TI GG+ P G E+GYF+ PT+ T D R+ Sbjct: 336 TEIGPLVSEEHFNKVTSYFDIATKEGATIAAGGE-PVG-EEGYFIRPTLFTDARNDMRIA 393 Query: 388 KEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHRVAGQIEAGIVWVNTW 447 +EEIFGPV+T IPF TE E L NDT YGL+ +WTNDL RA R ++EAG++WVN+ Sbjct: 394 QEEIFGPVLTSIPFTTEAEALALANDTAYGLTGYLWTNDLTRALRFTDRLEAGMIWVNSE 453 Query: 448 FLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNI 482 +R L TPFGG+K SGIGR+GG SFEFY E +I Sbjct: 454 NVRHLPTPFGGVKASGIGRDGGDWSFEFYMEQKHI 488 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: 631 Number of extensions: 31 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: 503 Length adjustment: 34 Effective length of query: 452 Effective length of database: 469 Effective search space: 211988 Effective search space used: 211988 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