Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate HSERO_RS05115 HSERO_RS05115 aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__HerbieS:HSERO_RS05115 Length = 793 Score = 328 bits (840), Expect = 5e-94 Identities = 183/462 (39%), Positives = 277/462 (59%), Gaps = 27/462 (5%) Query: 13 HFIDGKFV-PSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTAN 71 HFI G+F P D D+I+PA+ + L +++G AA++D AVQAA+ AL G W+ + + Sbjct: 35 HFIAGRFTQPKAD---LDDIDPASGKLLAHLSQGSAADVDAAVQAAQAALPG-WQALGGH 90 Query: 72 ERIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNE 131 R L + + L+VLE+LD GKP S +D+P A +F+ ++ + + +E Sbjct: 91 GRARHLYALARTVQRHARLLAVLETLDNGKPLRESRDVDVPLVARHFYHYAGWAQLQESE 150 Query: 132 ATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTAT 191 + PVGV+G I PWN PLL++ WK+APALA GNTVV+KPAE T +TA Sbjct: 151 ----------FPDHVPVGVVGQIVPWNFPLLMLAWKIAPALALGNTVVLKPAENTSLTAL 200 Query: 192 VLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTL 251 + AE+ + AG+P GV+N+V G G + GAA+ HP + I+FTG T G++I A + Sbjct: 201 LFAELAQQAGLPAGVLNIVTGDG--ATGAAVVAHPGIQKIAFTGSTEVGRLIREQTAGSG 258 Query: 252 KRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKF 311 K L+ ELGGK+P ++F D+++D IE + + + NQG+VC GSR+ V+ ++ F+ + Sbjct: 259 KSLTLELGGKSPFIVFEDADIDAAIEGVVDAIWFNQGQVCCAGSRLLVQEGIHDLFIARL 318 Query: 312 VAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGG----TILTGGKRPEGLE 367 + ++L VG P D + +GALIS ERV ++ V EG +L P G Sbjct: 319 KTRMQKLKVGAPLDKCSDMGALISPVQLERVRSLVEQGVREGAQCHQVVL---DTPPG-- 373 Query: 368 KGYFLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDL 427 G F PT++TG+ V EEIFGPV+ + F T +E ++ N++ YGL+AS+W+ + Sbjct: 374 -GCFYPPTLLTGVHPAATVASEEIFGPVLVAMSFRTPDEAVQLANNSRYGLAASIWSETI 432 Query: 428 RRAHRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGG 469 A VA Q++AG+VW+N+ D FGG+++SG GREGG Sbjct: 433 GLALGVAPQLKAGVVWINSTNQFDAAVGFGGVRESGYGREGG 474 Score = 72.0 bits (175), Expect = 7e-17 Identities = 69/248 (27%), Positives = 110/248 (44%), Gaps = 9/248 (3%) Query: 14 FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73 +I GK V DG+ + E+L V G +I AV AA KA G W + + R Sbjct: 521 YIGGKQVRP-DGEVSMACHSTQGERLEDVGLGNRKDIRNAVAAAVKA--GGWTSASPHRR 577 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPT-WLSGSIDIP-RAAYNFHFFSDYIRTITNE 131 L + + + R EE + + TG +D + + + ++D ++ Sbjct: 578 AQGLYYIAENLSARTEEFARRIASTTGVTADEARAEVDASIKRLFTYGAWADKFEGAVHQ 637 Query: 132 ATQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTAT 191 M VAL A+ +GV+G++ P PLL + +AP +A GN VV+ P+E P+ AT Sbjct: 638 PP-MRGVAL--AMPEAIGVVGVVCPEEKPLLALISLVAPLIAMGNRVVVVPSEQAPLVAT 694 Query: 192 VLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTL 251 L ++ + +P GV+N+V G L EH +V A+ G + L Sbjct: 695 DLYQVLDTSDLPAGVINIVTGKSAELL-PVLAEHDEVEALWVRGPAEFSATAERLSTGNL 753 Query: 252 KRLSYELG 259 KR + G Sbjct: 754 KRCFVDHG 761 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: 898 Number of extensions: 45 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 486 Length of database: 793 Length adjustment: 37 Effective length of query: 449 Effective length of database: 756 Effective search space: 339444 Effective search space used: 339444 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: 53 (25.0 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