Align succinate-semialdehyde dehydrogenase (NADP+) (EC 1.2.1.79); glyceraldehyde-3-phosphate dehydrogenase (NADP+) (EC 1.2.1.9) (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein
Query= BRENDA::Q97XA5 (470 letters) >NCBI__GCF_000012965.1:WP_011373513.1 Length = 471 Score = 255 bits (652), Expect = 2e-72 Identities = 157/458 (34%), Positives = 253/458 (55%), Gaps = 10/458 (2%) Query: 11 SPSNLKVIGTVKRMSKDEVRGEIEEAYKGFEIISRMPLYKRTAILRKISEILEREQERLA 70 +P N +V + D+ + + A + S+ + +R + L ++ L + +E +A Sbjct: 22 NPYNGEVASEFVTCNADDAKKALNIALLASKEASKTTIAQRCSWLLDVASKLAQNKEDIA 81 Query: 71 RLLAMEAGKPISDSRVEVLRASRLFRQAAEEVGIVLEGKNYRVDAYEYPPGNENRIVLST 130 + + E GKPI+ SR+EV R AAE + + G+ DA+ + I + Sbjct: 82 KTITDEVGKPITYSRIEVERCIETVTLAAETMR-TMHGETVNTDAFA---SGKKTISFFS 137 Query: 131 REPIGVVTAILPFNFPINSFAHKVAPALAVGNSVVVKPSINTPLAAVEMKKILVEAGLP- 189 R P GVV AI PFNFP+N AHK+APAL GN+V++KP+ PL A + K+ +E+ Sbjct: 138 RVPCGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESEFAI 197 Query: 190 DSAVRVVTGYSSEIGDEIITHPLVGLITLTGSTQTGLKIASKAISLGKRIIMELGGSDPI 249 A+ VV G +++G ++T + +I+ TGS G +I +K+ + K++ +ELGG+ Sbjct: 198 KDALSVVYG-DADVGGTLVTSEIPRVISFTGSVGVG-EIITKSAGI-KKVSLELGGNAAT 254 Query: 250 IILEDANIERASSIAVRARFEYAGQNCNAGKRIIVRQEVYDKFVKAFNEKAKALKVGEPL 309 I + AN++ A+ F +GQ C + +RI V +++Y +F E K L VG P Sbjct: 255 FIDKSANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLVVGSPY 314 Query: 310 DETTDVGPVINKESVENLNSVLEDAKVKGGRVEILNRGPESGSFFPLTMVTNPSLDMLVL 369 +E T +GP++N E+ + ++ A +K G IL E F+P M + DM ++ Sbjct: 315 EEDTFMGPLVNDEAAKRAMEWVQSA-IKEGATPILEPRVEGRVFYPCVMA-DVKEDMAIV 372 Query: 370 KSEVFGPIVPIVSVKSDEEAIRIANSTEYGLQSAIFTNDVNRALKLSRELKFGAVIINDS 429 EVF PIV ++ VK +EA+ + N++ YGLQ +IFTND+N + EL G ++IND Sbjct: 373 CQEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINELDAGGIVINDM 432 Query: 430 TRLRWDSLPFGGFKKTGIGREGVRETMLEMTENKLIAI 467 LR+D P+GG K +G+GREG R + EM+E K + I Sbjct: 433 PTLRFDIQPYGGVKLSGVGREGPRFAIEEMSEIKSVII 470 Lambda K H 0.316 0.135 0.366 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: 507 Number of extensions: 28 Number of successful extensions: 4 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: 470 Length of database: 471 Length adjustment: 33 Effective length of query: 437 Effective length of database: 438 Effective search space: 191406 Effective search space used: 191406 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 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Apr 09 2024. 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