Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate AO356_25585 AO356_25585 2-hydroxymuconic semialdehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25585 Length = 486 Score = 453 bits (1166), Expect = e-132 Identities = 228/479 (47%), Positives = 322/479 (67%), Gaps = 11/479 (2%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 H+IDG+ V S D F N NPAT E +G VA GGA E+ AV AAK+A W A E Sbjct: 4 HWIDGREVESKD--VFVNYNPATGEAIGEVASGGAEEVAQAVAAAKEAFP-KWANTPAKE 60 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R ++RK+G+LI + +L+ LE+LDTG P + ++ IPRA++NF FF++ + Sbjct: 61 RARLMRKLGELIEQNVPKLAELETLDTGLPIHQTKNVLIPRASHNFDFFAEVCTRMDGHT 120 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 +DD LNY + +PVGV L++PWN+P + TWK AP LA GNT V+K +EL+P+TA Sbjct: 121 YPVDDQMLNYTLYQPVGVCALVSPWNVPFMTATWKTAPCLALGNTAVLKMSELSPLTANE 180 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 L + +AG+P+GV+N++ G+G +AG AL HPDV AISFTG T TGK IM +A LK Sbjct: 181 LGRLAVEAGIPNGVLNVIQGYGA-TAGDALVRHPDVRAISFTGGTATGKKIMQTAG--LK 237 Query: 253 RLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFV 312 + S ELGGK+P +IF D++L+ ++ + + F GE C GSRI+++ Y F+ +F Sbjct: 238 KYSMELGGKSPVLIFEDADLERALDAALFTIFSLNGERCTAGSRIFIQESVYPQFVAEFA 297 Query: 313 AKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGG-----KRPEGLE 367 A+ K L+VGDP D KT+VG++I+ HY++VTGYIK+ +EEG T+L GG P L Sbjct: 298 ARAKRLIVGDPQDPKTQVGSMITQAHYDKVTGYIKIGLEEGATLLAGGLERPANLPAHLS 357 Query: 368 KGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDL 427 G F++PT+ + R+ +EEIFGPVV +IPF E E L+ NDT YGL++ +WT D+ Sbjct: 358 HGQFIQPTVFADVNNKMRIAQEEIFGPVVCLIPFKDEAEALQLANDTEYGLASYIWTQDI 417 Query: 428 RRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486 +AHR+A IEAG+V++N+ +RDLR PFGG+K SG GREGG +SFE ++E+ N+CI + Sbjct: 418 GKAHRLAHGIEAGMVFINSQNVRDLRQPFGGVKGSGTGREGGQYSFEVFAEIKNVCISM 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: 624 Number of extensions: 29 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: 486 Length adjustment: 34 Effective length of query: 452 Effective length of database: 452 Effective search space: 204304 Effective search space used: 204304 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