Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate CA265_RS24850 CA265_RS24850 aldehyde dehydrogenase
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__Pedo557:CA265_RS24850 Length = 454 Score = 224 bits (571), Expect = 5e-63 Identities = 145/437 (33%), Positives = 220/437 (50%), Gaps = 9/437 (2%) Query: 31 INPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANERIAVLRKVGDLILERKEE 90 INPAT E + ++ E + + L A +KA W T ERIAV+ DL+ E+ Sbjct: 4 INPATAEIITSLEEDNLSTLQLKFDALQKA-QPQWAGKTLQERIAVITHFSDLLEVEIEK 62 Query: 91 LSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEATQMDDVALNYAIR-RPVG 149 L+ + + + GKP S + +I A + + D+ + I+ P+G Sbjct: 63 LASVLTSEVGKPLQQSRN-EINGARARIKWMLANAEKYLADEVMTDEPGIKEIIKYEPLG 121 Query: 150 VIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTATVLAEICRDAGVPDGVVNL 209 V+ I+ WN P L+ PAL +GNTV+ KP+E +T + ++ + AGVPD V ++ Sbjct: 122 VVCNISAWNYPYLVGVNVFIPALLSGNTVMYKPSEYATLTGIEIEKLLKKAGVPDDVFHI 181 Query: 210 VHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKTLKRLSYELGGKNPNVIFAD 269 G G+AL + D N FTG TGK+I A + ELGGK+P I D Sbjct: 182 A--IGAKETGSALL-NMDFNGYFFTGSYKTGKLIYEKVAAKMVPCQLELGGKDPLYITDD 238 Query: 270 -SNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEKFVAKTKELVVGDPFDAKT 328 +++ T +F N G+ C RIYV+ Y+ + FV + K G P Sbjct: 239 VTDVAAAAIGTADGAFYNNGQSCCAVERIYVQEKNYDDYCNAFVTEVKSWKTGIPTAEGV 298 Query: 329 KVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGYFLEPTIITGLTRDCRVVK 388 +GAL E + +K A+ +G +LTGGK EG KGY+ EPT++T +T D V++ Sbjct: 299 YIGALTRKEQISVLENQVKDALNKGAKLLTGGKAVEG--KGYYFEPTVLTDVTNDMLVMQ 356 Query: 389 EEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRAHRVAGQIEAGIVWVNTWF 448 EE FGP++ ++ + E L+ + DT YGL+ASV+T RA ++ Q++AG + N Sbjct: 357 EESFGPIIGIMKVKDDAEALKMMKDTDYGLTASVYTASQERAEKILAQLDAGSGYWNCCD 416 Query: 449 LRDLRTPFGGMKQSGIG 465 P+ G K SGIG Sbjct: 417 RVSAALPWSGRKYSGIG 433 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: 511 Number of extensions: 27 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: 454 Length adjustment: 33 Effective length of query: 453 Effective length of database: 421 Effective search space: 190713 Effective search space used: 190713 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: 51 (24.3 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