Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate GFF882 Psest_0905 NAD-dependent aldehyde dehydrogenases
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__psRCH2:GFF882 Length = 499 Score = 399 bits (1026), Expect = e-116 Identities = 208/475 (43%), Positives = 300/475 (63%), Gaps = 5/475 (1%) Query: 14 FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73 FID ++V G+T D INPA + L + AA++D AVQAA++A W+ + ER Sbjct: 20 FIDNQWVSDEYGETLDIINPANGKILTNIPNATAADVDRAVQAAQRAFM-TWRTTSPAER 78 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133 L K+ DL+ + +VLE+LD GKP S S+DIP A +F +F+ IR+ ++EA Sbjct: 79 ANALLKIADLLEADADRFAVLETLDVGKPIRESRSVDIPLAIDHFRYFAGVIRSQSDEAV 138 Query: 134 QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVL 193 +D+ L+ A+ P+GV+G + PWN PLL+ WK+APA+AAGNTVV+KP+ELTP+T L Sbjct: 139 MLDEQTLSIALSEPLGVVGQVIPWNFPLLMAAWKIAPAIAAGNTVVIKPSELTPVTILEL 198 Query: 194 AEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKR 253 A+I +P GVVN+V G G + G AL +HPD+ ++FTG T G+++ +AAK + Sbjct: 199 AKIFAKV-LPAGVVNIVTGLG-TTVGQALLDHPDLRKLAFTGSTRVGELVANAAAKKIIP 256 Query: 254 LSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVA 313 + ELGGK+ N++F D+N D+ +E + + NQG+VC G+R++V YE FL + Sbjct: 257 ATLELGGKSANIVFPDANWDKAVEGAVLAILWNQGQVCESGARLFVHESIYERFLAELKH 316 Query: 314 KTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEG--LEKGYF 371 K + + VGDP + T +GA +S ER+ GY+ +A +EG +L GG R G + G+F Sbjct: 317 KFEAVRVGDPLNPDTMMGAQVSKSQMERILGYVDIAKQEGAEVLIGGGRLTGANYDAGFF 376 Query: 372 LEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAH 431 ++PTI+ G+ D RV EEIFGPV+ VIPF E EV+ ND+ YGL+ +VWT D+ RA Sbjct: 377 IQPTILVGVRNDMRVAYEEIFGPVLCVIPFKDEAEVIAMANDSEYGLAGAVWTQDINRAL 436 Query: 432 RVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486 RVA +E G +WVNT+ PFGG K+SG+GRE E YS+ NI + L Sbjct: 437 RVARAVETGRMWVNTYHEIPAHAPFGGYKKSGLGRETHKSMLEAYSQKKNIYVSL 491 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: 635 Number of extensions: 32 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: 499 Length adjustment: 34 Effective length of query: 452 Effective length of database: 465 Effective search space: 210180 Effective search space used: 210180 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