Align Aldehyde dehydrogenase 5, mitochondrial; EC 1.2.1.5 (characterized)
to candidate Echvi_1300 Echvi_1300 delta-1-pyrroline-5-carboxylate dehydrogenase, group 1
Query= SwissProt::P40047 (520 letters) >FitnessBrowser__Cola:Echvi_1300 Length = 543 Score = 176 bits (446), Expect = 2e-48 Identities = 137/433 (31%), Positives = 210/433 (48%), Gaps = 19/433 (4%) Query: 83 VDEAVAAAKKAFETKWSIVEPEVRAKALFNLADLVE-KHQETLAAIESMDNGKSLFCARG 141 V++A+ AA A E W +E E RA ADL+ ++ + A + K+ F A Sbjct: 81 VEQAINAALGAKEA-WETMEWEQRAAIFLKAADLIAGPYRYKMNAATMLGQSKNAFQAEI 139 Query: 142 DVAL-VSKYLRSCGGWADKIYGNVID-TGKNHFTYSIKEPL-GVCGQIIPWNFPLLMWSW 198 D A + +LR + +IY +G + + PL G + P+NF + + Sbjct: 140 DSACEIVDFLRFNVKYMTEIYKQQPPISGDGVWNRLEQRPLEGFVFALTPFNFTAIAGNL 199 Query: 199 KIGPALATGNTVVLKPAETTPLSALFASQLCQEAGIPAGVVNILPGSGRVVGERLSAHPD 258 PA+ GNTVV KPA T +A Q+ +EAG+P GV+N++ G GE + HP+ Sbjct: 200 PTAPAMM-GNTVVWKPAYTQIYTANLLMQVFREAGVPDGVINLVYVDGPAAGEVIFEHPE 258 Query: 259 VKKIAFTGSTATGRHIMKVAADTVKK------VTLELGGKSPNIVFADADLDKAVKNIAF 312 I FTGSTA + I K + ++K + E GGK I AD + + Sbjct: 259 FAGIHFTGSTAVFQTIWKTIGNNIEKYKSYPRIVGETGGKDFVIAHKSADAKQLATGLVR 318 Query: 313 GIFYNSGEVCCAGSRIYIQDTVYEEVLQKLKDYTESLKVGDPFDEEVFQGAQTSDKQLHK 372 G F G+ C A SR YI ++E+V + +++ S+K+G P D F A +K K Sbjct: 319 GAFEFQGQKCSAASRAYIPSNLWEDVKKYMQEDLASIKMGGPEDFSNFINAVIDEKSFDK 378 Query: 373 ILDYVDVAKSEGARLVTGGARHGSKGYFVKPTVFADVKEDMRIVKEEVFGPIVTVSKFST 432 I Y+D AKS+G +V GG SKGYFV+PTV + EE+FGP++T+ + Sbjct: 379 IAKYIDTAKSDGLEVVAGGHYDKSKGYFVEPTVLLTKDPMYTTMCEEIFGPVLTIYVYQE 438 Query: 433 --VDEVIAMAND-SQYGLAAGIHTNDINKAVDVSKRVK--AGTVWIN--TYNNFHQNVPF 485 +E + + + S YGL I ++D A +++++ AG +IN PF Sbjct: 439 DHFEEALELVDQTSPYGLTGAIFSHDRYAAQLATQKLRNAAGNFYINDKPTGAVVGQQPF 498 Query: 486 GGFGQSGIGREMG 498 GG +SG + G Sbjct: 499 GGARKSGTNDKAG 511 Lambda K H 0.317 0.134 0.390 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: 667 Number of extensions: 35 Number of successful extensions: 2 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: 520 Length of database: 543 Length adjustment: 35 Effective length of query: 485 Effective length of database: 508 Effective search space: 246380 Effective search space used: 246380 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