Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Echvi_1300 Echvi_1300 delta-1-pyrroline-5-carboxylate dehydrogenase, group 1
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__Cola:Echvi_1300 Length = 543 Score = 166 bits (421), Expect = 2e-45 Identities = 133/441 (30%), Positives = 201/441 (45%), Gaps = 19/441 (4%) Query: 70 EGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADLIERDRTY-LAALETLDNG 128 EGDK V++A+ AA A + W M+ R + + ADLI Y + A L Sbjct: 75 EGDKSHVEQAINAALGAKEA---WETMEWEQRAAIFLKAADLIAGPYRYKMNAATMLGQS 131 Query: 129 KPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGD-FFSYTRHEPV-GVCGQIIPWN 186 K + + ++ LR+ + + + + PI GD ++ P+ G + P+N Sbjct: 132 KNAFQAEIDSACEIVDFLRFNVKYMTEIYKQQPPISGDGVWNRLEQRPLEGFVFALTPFN 191 Query: 187 FPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAGFPPGVVNIVPGFGPTAG 246 F + PA+ GN VV K A TA + + +EAG P GV+N+V GP AG Sbjct: 192 FTAIAGNLPTAPAMM-GNTVVWKPAYTQIYTANLLMQVFREAGVPDGVINLVYVDGPAAG 250 Query: 247 AAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLK-----RVTLELGGKSPNIIMSDADMD 301 I H + + FTGST + + I G++ K R+ E GGK I AD Sbjct: 251 EVIFEHPEFAGIHFTGSTAVFQTIWKTIGNNIEKYKSYPRIVGETGGKDFVIAHKSADAK 310 Query: 302 WAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVGNPFDSKTEQGPQ 361 F QGQ C A SR ++ +++++ + S +G P D Sbjct: 311 QLATGLVRGAFEFQGQKCSAASRAYIPSNLWEDVKKYMQEDLASIKMGGPEDFSNFINAV 370 Query: 362 VDETQFKKILGYINTGKQEGAKLLCGGGIAADRGYFIQPTVFGDVQDGMTIAKEEIFGPV 421 +DE F KI YI+T K +G +++ GG +GYF++PTV T EEIFGPV Sbjct: 371 IDEKSFDKIAKYIDTAKSDGLEVVAGGHYDKSKGYFVEPTVLLTKDPMYTTMCEEIFGPV 430 Query: 422 MQILKFKT--IEEVVGRAN-NSTYGLAAAVFTKDLDKANYLSQALQ--AGTVWVNCYDVF 476 + I ++ EE + + S YGL A+F+ D A +Q L+ AG ++N Sbjct: 431 LTIYVYQEDHFEEALELVDQTSPYGLTGAIFSHDRYAAQLATQKLRNAAGNFYINDKPTG 490 Query: 477 G--AQSPFGGYKMSGSGRELG 495 Q PFGG + SG+ + G Sbjct: 491 AVVGQQPFGGARKSGTNDKAG 511 Lambda K H 0.319 0.136 0.409 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: 658 Number of extensions: 37 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: 517 Length of database: 543 Length adjustment: 35 Effective length of query: 482 Effective length of database: 508 Effective search space: 244856 Effective search space used: 244856 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