Align α-ketoglutaric semialdehyde dehydrogenase subunit (EC 1.2.1.26) (characterized)
to candidate Echvi_3952 Echvi_3952 NAD-dependent aldehyde dehydrogenases
Query= metacyc::G1G01-1343-MONOMER (525 letters) >FitnessBrowser__Cola:Echvi_3952 Length = 478 Score = 422 bits (1085), Expect = e-122 Identities = 239/470 (50%), Positives = 297/470 (63%), Gaps = 6/470 (1%) Query: 53 AAFDAYRETSLEQRAEFLEAIATQIEALGDALIDRAVIETGLPKARIQGERGRTCTQLRT 112 AAF+ Y+ TSL +RA FL IA Q+EA+ +ALI A E+ LP+ RI GE GRT Q+R Sbjct: 12 AAFEQYKITSLAERAAFLRKIADQLEAIKEALIPTACEESHLPEGRITGELGRTTGQIRL 71 Query: 113 FARTVRAGEWLDVRIDSALPERQPLPRADLRQRQVALGPVAVFGASNFPLAFSVAGGDTA 172 FA+ V G WL+V ID PER P P+ DLR+ V LGPVAVFGASNFPLAFS AGGD+ Sbjct: 72 FAKYVEEGTWLEVTIDHGDPERTPAPKPDLRRMLVPLGPVAVFGASNFPLAFSTAGGDSI 131 Query: 173 SALAAGCPVVVKAHSAHPGTSELVGQAVAQAVKQCGLPEGVFSLLYGSGREVGIALVSDP 232 SALAAGC VV K H HP TS +V +A+ QA+ GLPEGVF + G G G LV P Sbjct: 132 SALAAGCTVVYKGHPGHPKTSLMVFEAIQQAIAAAGLPEGVFQHVEG-GISEGQTLVQHP 190 Query: 233 RIKAVGFTGSRSGGMALCQAAQARPEPIPVYAEMSSINPVFLFDAALQARAEALAQGFVA 292 IKAVGFTGS GG AL A +RPEPIPVYAEM SINP+ F++AL A +E +A + Sbjct: 191 AIKAVGFTGSFKGGKALFDLANSRPEPIPVYAEMGSINPIIAFESAL-ANSEQVAGQYAQ 249 Query: 293 SLTQGAGQFCTNPGLVIARQGPALQRFITAAAGYVQQGAAQTMLTPGIFSAYQAGIAALA 352 SLT GAGQFCTNPG++ A + F + A Q ML GI +AY + LA Sbjct: 250 SLTLGAGQFCTNPGVIFVPADMA-EAFAQNTGKVLADAAGQAMLHEGIQTAYHQSLDHLA 308 Query: 353 DNPHAQAITSGQAGQGPNQCQAQLFVTQAEAFLADPALQAEVFGAASLVVACTDDEQVRQ 412 D + I A + L +T + ++ P+LQ EVFG +VVA + + Sbjct: 309 DTGGLKWIQKAAAKDAGHPA---LALTDLDTWIKSPSLQEEVFGPFGIVVAYDSIAALLK 365 Query: 413 VAEHLEGQLTATLQLDEADIDSARALLPTLERKAGRILVNGWPTGVEVCDAMVHGGPFPA 472 A+ L+GQLT TL E+++ AL+ TL+ K GR+L G PTGVEV AM HGGPFPA Sbjct: 366 AAKTLQGQLTITLWASESELTDQAALINTLQDKCGRLLFGGVPTGVEVGHAMQHGGPFPA 425 Query: 473 TSDARTTSVGTAAILRFLRPVCYQDVPDALLPQALKHGNPLQLRRLLDGK 522 T+D+R+TSVG AI RF RP YQ+ PD LLP+ LK NPL + R +DG+ Sbjct: 426 TTDSRSTSVGVYAIKRFARPFAYQNCPDGLLPKELKEANPLDIIRTVDGE 475 Lambda K H 0.319 0.134 0.391 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: 686 Number of extensions: 37 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: 525 Length of database: 478 Length adjustment: 34 Effective length of query: 491 Effective length of database: 444 Effective search space: 218004 Effective search space used: 218004 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 (21.8 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