Align 2-hydroxymuconate-6-semialdehyde dehydrogenase (EC 1.2.1.85) (characterized)
to candidate 6938534 Sama_2637 succinate-semialdehyde dehydrogenase (NAD(P)(+)) (RefSeq)
Query= metacyc::MONOMER-15108 (486 letters) >FitnessBrowser__SB2B:6938534 Length = 480 Score = 305 bits (781), Expect = 2e-87 Identities = 176/476 (36%), Positives = 275/476 (57%), Gaps = 12/476 (2%) Query: 14 FIDGKFVPSLDGKTFDNINPATEEKLGTVAEGGAAEIDLAVQAAKKALNGPWKKMTANER 73 +I+G++ +L G+T NPAT E + +V G E A+ AA+ AL W+ +TA ER Sbjct: 14 YINGEWRDALSGETVTIANPATNEAIASVPVMGRDETREAIAAAEAALPA-WRALTAKER 72 Query: 74 IAVLRKVGDLILERKEELSVLESLDTGKPTWLSGSIDIPRAAYNFHFFSDYIRTITNEAT 133 A LR+ +L+LE ++L+++ + + GKP ++ AA +F++ + + + Sbjct: 73 GAKLRRWYELMLENADDLALMMTTEQGKPL-AEAKGEVVYAASFIEWFAEEAKRLYGDTI 131 Query: 134 ---QMDDVALNYAIRRPVGVIGLINPWNLPLLLMTWKLAPALAAGNTVVMKPAELTPMTA 190 Q D + I++ VGV I PWN P ++T K PALAAG T+++KPA TP TA Sbjct: 132 PGHQGDKRIM--VIKQGVGVTAAITPWNFPAAMITRKAGPALAAGCTMIVKPAPQTPFTA 189 Query: 191 TVLAEICRDAGVPDGVVNLVHGFGPNSAGAALTEHPDVNAISFTGETTTGKIIMASAAKT 250 LAE+ +AG+P GV ++V G + G L E+P V +SFTG T G +M A T Sbjct: 190 LALAELAAEAGIPPGVFSVVTGDAV-AIGNELCENPVVRKLSFTGSTGVGIKLMQQCAPT 248 Query: 251 LKRLSYELGGKNPNVIFADSNLDEVIETTMKSSFINQGEVCLCGSRIYVERPAYEAFLEK 310 LK++S ELGG P ++F D++LD +E M S + N G+ C+C +R+YV+ Y+AF +K Sbjct: 249 LKKVSLELGGNAPFIVFNDADLDAAVEGAMISKYRNAGQTCVCANRLYVQDGVYDAFAQK 308 Query: 311 FVAKTKELVVGDPFDAKTKVGALISDEHYERVTGYIKLAVEEGGTILTGGKRPEGLEKGY 370 A +L VG+ + G LI+ E+V +++ A+++G T++ GGK P G G Sbjct: 309 LAAAVAKLKVGNGAEPGVTTGPLINAAALEKVQSHLQDALDKGATLVAGGK-PLG---GN 364 Query: 371 FLEPTIITGLTRDCRVVKEEIFGPVVTVIPFDTEEEVLEQINDTHYGLSASVWTNDLRRA 430 F+EP I+T + +V +EE FGP+ + F ++V+ Q NDT +GL+A + D+ Sbjct: 365 FMEPAIVTNVDASMKVAREETFGPLAPLFRFSDVDDVIRQANDTEFGLAAYFYGRDISLI 424 Query: 431 HRVAGQIEAGIVWVNTWFLRDLRTPFGGMKQSGIGREGGLHSFEFYSELTNICIKL 486 +VA +E G+V VNT + PFGGMK SG+GREG + + Y E+ IC+ + Sbjct: 425 WKVAEALEYGMVGVNTGLISTEVAPFGGMKSSGLGREGSKYGIDEYVEIKYICLSV 480 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: 576 Number of extensions: 32 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: 480 Length adjustment: 34 Effective length of query: 452 Effective length of database: 446 Effective search space: 201592 Effective search space used: 201592 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