Align 2-hydroxymuconic semialdehyde dehydrogenase; HMSD; EC 1.2.1.85 (characterized)
to candidate Synpcc7942_0489 Synpcc7942_0489 aldehyde dehydrogenase
Query= SwissProt::P23105 (486 letters) >FitnessBrowser__SynE:Synpcc7942_0489 Length = 459 Score = 140 bits (354), Expect = 7e-38 Identities = 105/344 (30%), Positives = 165/344 (47%), Gaps = 18/344 (5%) Query: 139 YGVRRPKGVIGVISPWNLPLLLMTWKVGPALACGNCVVVKPSEETPLTATLLGEVMQAAG 198 Y P GV+ +I PWN P L+ + A+A GNC V+KPSE P T++L+ ++ Sbjct: 104 YRQAEPLGVVLIIGPWNYPFQLLITPLIGAIAAGNCAVLKPSELAPATSSLIQRLISDRF 163 Query: 199 VPAGVYNVVHGFGGDSAGAFLTEHPDVDAYTFTGETGTGETIMRAAAKGVRQVSLELGGK 258 P + + GD++ + D FTG T G +M AAA+ + V+LELGGK Sbjct: 164 DP----DYIRVLEGDASVSQALITQPFDHIFFTGGTAIGRKVMAAAAENLTPVTLELGGK 219 Query: 259 NAGIVFADCDMDKAIEGTLRSAFANCGQVCLGTERVYVERPIFDAFVARLKAGAEALKIG 318 + IV D D+D A F N GQ C+ + + V+R + + F+ L + G Sbjct: 220 SPCIVDTDIDLDVAARRIAWGKFFNAGQTCIAPDYLLVQRTVAEPFIEALIDNIQQF-YG 278 Query: 319 EPNDPEANFGPLISHKPREKVPSYYQQAVDDGATVVTGGGVPEMPAHLAGGAWVQPTIWT 378 E A++ ++S + +++ S + DG T+ GG V ++A PT+ T Sbjct: 279 EDPQQSADYARIVSDRHWQRLNS----LLVDG-TIRHGGQVDRSDRYIA------PTLIT 327 Query: 379 GLADDSAVVTEEIFGPCCHIRPFDSEEEAIELANSLPYGLASAIWTENVRRAHRVAGQIE 438 + ++ EEIFGP I +D +EAI + P LA +++ + + RV + Sbjct: 328 DVNWRDPILQEEIFGPLLPILIYDQLDEAIAQIRAQPKPLALYLFSRDRQVQERVLAETS 387 Query: 439 AGIVWVNSWFLR--DLRTAFGGSKQSGIGREGGVHSLEFYTELK 480 AG V +N L+ AFGG SG+G G S E ++ K Sbjct: 388 AGSVCLNDTILQVGVPDAAFGGVGPSGMGGYHGKASFETFSHYK 431 Lambda K H 0.318 0.136 0.413 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: 460 Number of extensions: 20 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: 459 Length adjustment: 33 Effective length of query: 453 Effective length of database: 426 Effective search space: 192978 Effective search space used: 192978 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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