Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate 3608018 Dshi_1425 aldehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Dino:3608018 Length = 484 Score = 285 bits (730), Expect = 2e-81 Identities = 170/469 (36%), Positives = 253/469 (53%), Gaps = 13/469 (2%) Query: 13 HFIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANE 72 H I+G V S +F+ NPAT+E + +++ A+ AAK A G W ++ +E Sbjct: 21 HAINGALVDSAG--SFEVFNPATDEVVAHAPNASRDQVEQAIAAAKAAQPG-WAALSQDE 77 Query: 73 RIAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEA 132 R A + D + K+EL L + + GKP + ++ A + + R + +E Sbjct: 78 RGAYIAAYADALDAHKQELITLLTTEQGKPRHSMATTEVEYAIFWVREVAK--RRLEDEV 135 Query: 133 TQMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATV 192 + P+GV+G I PWN P+LL WK+AP L GNT+VMKP+ TP+ Sbjct: 136 IEDTPEHTVKVAHTPLGVVGAITPWNFPVLLGLWKIAPCLVTGNTMVMKPSPYTPLCTLR 195 Query: 193 LAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLK 252 EI + P GV+N+V G N GA LTEHPD+ ISFTG T TG+ +MAS++ LK Sbjct: 196 FGEIAQQV-FPAGVLNVVAG--GNEQGAWLTEHPDIAKISFTGSTATGRKVMASSSCNLK 252 Query: 253 RLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFV 312 R++ ELGG +P ++ ++ +I T +++ N G+ C+ R+YV Y+ FL FV Sbjct: 253 RITLELGGNDPAILLPGTDYKPLIPTLFDAAYGNSGQWCIAVKRLYVHESLYDDFLRDFV 312 Query: 313 AKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFL 372 A E VG+ D T +G + + Y ++ +G ++ GG+ P+G G F+ Sbjct: 313 AHAAEKTVGNGMDPNTDLGPIQNKMQYGKLKDLFADVKAQGLSVPLGGEIPDG--PGNFV 370 Query: 373 EPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHR 432 TI+ +D RVV+EE FGP++ +I + +EV+ NDT +GL+ASVW D A Sbjct: 371 PITIVDNPPKDSRVVREEPFGPILPIIKWSDLDEVVRDANDTEFGLAASVWGPDRDTAIG 430 Query: 433 VAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTN 481 VA ++EAG VWVN + + PFGG KQSG+G E G E E TN Sbjct: 431 VANRLEAGTVWVNEIHIHGIDIPFGGHKQSGMGVENGQ---EGLKEFTN 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: 581 Number of extensions: 31 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: 484 Length adjustment: 34 Effective length of query: 452 Effective length of database: 450 Effective search space: 203400 Effective search space used: 203400 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