Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Cola:Echvi_0481 Length = 509 Score = 375 bits (963), Expect = e-108 Identities = 201/481 (41%), Positives = 293/481 (60%), Gaps = 14/481 (2%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 +FI GKFVP +DG+ FD I+P + VA G AA+I+LA+ AA KA W + +A E Sbjct: 24 NFIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELALDAAHKAFPA-WSRTSATE 82 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R +L K+ D I + E L+ +E++D GKP + + D+ +F +F+ IR Sbjct: 83 RSNILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAGVIRAEEGSI 142 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 ++D ++ ++ P+G++G I PWN P+L+ TWK+APALAAG ++KPAE TP + + Sbjct: 143 AELDQHTVSVNVKEPIGIVGQIIPWNFPMLMATWKMAPALAAGCCTIVKPAEQTPASIMI 202 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 L E+ D +P GV+N+V+GFGP AG L + P ++ ++FTGETTTG++IM A++ L Sbjct: 203 LMEVIGDL-LPAGVLNVVNGFGP-EAGKPLAQSPRLDKVAFTGETTTGRLIMQYASENLN 260 Query: 253 RLSYELGGKNPNVIFA------DSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEA 306 ++ ELGGK+PNV F D LD+ +E + + +NQGEVC C SRI V Y+A Sbjct: 261 PVTMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFA-LNQGEVCTCPSRILVHEKIYDA 319 Query: 307 FLEKFVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGG---KRP 363 F+EK +A+ + + +G P D T +GA S + +E++ YI + +EG +LTGG K Sbjct: 320 FMEKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQEGAEVLTGGEVAKLN 379 Query: 364 EGLEKGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVW 423 GLE GY+++PT++ G + RV +EEIFGPV +V F EE + NDT YGL A VW Sbjct: 380 SGLENGYYVKPTLLKGHNK-MRVFQEEIFGPVCSVATFKDVEEAISISNDTLYGLGAGVW 438 Query: 424 TNDLRRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNIC 483 T D A++V I+AG VWVN + PFGG K+SG GRE L Y + N+ Sbjct: 439 TRDAHEAYQVPRAIKAGRVWVNCYHAYPAHAPFGGYKKSGFGRETHLMMLNHYRQNKNML 498 Query: 484 I 484 I Sbjct: 499 I 499 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: 628 Number of extensions: 35 Number of successful extensions: 7 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: 509 Length adjustment: 34 Effective length of query: 452 Effective length of database: 475 Effective search space: 214700 Effective search space used: 214700 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