Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate HSERO_RS05710 HSERO_RS05710 aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__HerbieS:HSERO_RS05710 Length = 486 Score = 323 bits (827), Expect = 1e-92 Identities = 188/472 (39%), Positives = 277/472 (58%), Gaps = 12/472 (2%) Query: 14 FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73 +IDGK+ P + + PATEE++ +A G AA++D AVQAA++A+ W + ER Sbjct: 19 YIDGKWQPPQGSERAAVVAPATEERVCEIALGNAADVDQAVQAARRAIPA-WAATSPLER 77 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133 A+L +V L+LER E + +L+ G P + + +P AA + D + + Sbjct: 78 AALLGRVHALLLERSELFAQALTLEMGAPISYARTAHVPLAAEHLRVARDNLA----DYP 133 Query: 134 QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVL 193 + +R P+GV LI PWN P+ +T K+ PALAAG TVV+KP+EL+P++A + Sbjct: 134 FIRPRGTTAIVREPIGVCALITPWNWPIYQITAKVGPALAAGCTVVLKPSELSPLSALLF 193 Query: 194 AEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKR 253 AEI +AGVP GV NLV+G G GAAL+ HP V+ IS TG T G ++ +AA T+KR Sbjct: 194 AEIVHEAGVPAGVFNLVNGSGAE-VGAALSAHPQVDMISITGSTRAGVLVAQAAAVTVKR 252 Query: 254 LSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVA 313 ++ ELGGK+PN++ D++L+ I + ++ N G+ C +R+ V R A E +A Sbjct: 253 VAQELGGKSPNLVLPDADLERAIPPGVAAALRNMGQSCSAPTRLIVPRAALARVHELALA 312 Query: 314 KTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGK-RPEGLEKGYFL 372 ++ VGDP DA T G L + + RV I+ +++G +L GG RP+GL +GY+ Sbjct: 313 TLAQMKVGDPNDAATTHGPLANRAQFLRVQQMIEAGLQDGARLLAGGPGRPDGLAQGYYA 372 Query: 373 EPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHR 432 PTI + + D + +EEIFGPV+ ++P+DT EE + NDT YGL A V D + Sbjct: 373 RPTIFSEVHTDMVIAQEEIFGPVLAILPYDTVEEAIAIANDTVYGLGAHVQGRDKDQVRA 432 Query: 433 VAGQIEAGIVWVN--TWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNI 482 VA +I++G V +N W D + PFGG KQSG GRE G+ E Y E+ I Sbjct: 433 VAARIQSGQVHLNYPAW---DPQAPFGGYKQSGNGREYGVEGMEEYMEVKAI 481 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: 515 Number of extensions: 20 Number of successful extensions: 6 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 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