Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate WP_058929223.1 AU252_RS01555 aldehyde dehydrogenase
Query= SwissProt::O34660 (495 letters) >NCBI__GCF_001484605.1:WP_058929223.1 Length = 508 Score = 427 bits (1099), Expect = e-124 Identities = 225/495 (45%), Positives = 312/495 (63%), Gaps = 13/495 (2%) Query: 8 VTKRLETFLQGTKKLYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKAAR 67 V +R + + IDG +V S+SG TF +P + + A DVD+AV+AAR Sbjct: 9 VAERFSVESDRSYSMLIDGAWVQSSSGETFACVDPYDNASWGRVPAATVEDVDRAVRAAR 68 Query: 68 KAFDQGEWRTMSPASRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAIEH 127 +AFD+G W P+ R+ L+ + ADL+ E+ ELA+ + +NGK I E T G + + +H Sbjct: 69 RAFDEGGWPQTLPSQRAALLRRFADLLTENADELARGQIHENGKLIGEMTWGALQMG-QH 127 Query: 128 MRYYAGWCTKITGQTI----PVSGAYFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAALA 183 Y AG I G+TI P + A+ T EP+GVV I PWN PL++ WK+ AALA Sbjct: 128 AHYVAGLAETIQGRTIESNWPNTAAF---TFREPIGVVAMITPWNSPLMLLSWKLFAALA 184 Query: 184 TGCTIVLKPAEQTPLSALYLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIAFT 243 G T+V+KP+E TP S L +AEL +AGFP GVIN++ GFG+ G AL +H VDKIAFT Sbjct: 185 AGNTVVIKPSEATPTSTLRMAELAMEAGFPPGVINVVTGFGQPTGSALVDHRGVDKIAFT 244 Query: 244 GSTEIGKKIMSTAAKSIKRVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQGQVCCAG 303 GST G+ I AA+ RVTLELGGKSPNI+ DA++ A+ GA+ G+ GQ C G Sbjct: 245 GSTSAGRAINKQAAERFARVTLELGGKSPNIIFSDADIDNAVHGAMAGIFGATGQTCMGG 304 Query: 304 SRVFIHKDQYDEVVDEMASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDEGA 363 SRV + YD+ VD MA ++L G L +GP+ ++ Q ++V+ Y+ G+ EGA Sbjct: 305 SRVLVQDSIYDDFVDRMARATQALTLGDPLDPTVDMGPVSNRAQFQKVIDYVDLGQSEGA 364 Query: 364 KAVTGG-----SCPFEAGYFVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERA 418 + V GG + G F PTVFANV +E +A+EEIFGPV + I + DE ++ A Sbjct: 365 EVVAGGARCMTTSELSKGLFFEPTVFANVSNESRLAQEEIFGPVASIIRFRDEDEAVKIA 424 Query: 419 NHSEYGLAAGLWTENVKQAHYIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGREMGSY 478 N S++GLAAG+WT +V +AH + R+++GTVWVN Y + + + PFGG+KQSG+GRE+G Sbjct: 425 NASDFGLAAGVWTNDVSRAHRMIRRVRSGTVWVNTYRLTNYSVPFGGFKQSGIGRELGPD 484 Query: 479 ALDNYTEVKSVWVNL 493 ALD YTEVKS W++L Sbjct: 485 ALDAYTEVKSAWIDL 499 Lambda K H 0.316 0.133 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: 599 Number of extensions: 19 Number of successful extensions: 3 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: 495 Length of database: 508 Length adjustment: 34 Effective length of query: 461 Effective length of database: 474 Effective search space: 218514 Effective search space used: 218514 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: 52 (24.6 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