Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate WP_011318370.1 AVA_RS07875 aldehyde dehydrogenase family protein
Query= SwissProt::O34660 (495 letters) >NCBI__GCF_000204075.1:WP_011318370.1 Length = 498 Score = 336 bits (862), Expect = 1e-96 Identities = 187/478 (39%), Positives = 283/478 (59%), Gaps = 11/478 (2%) Query: 23 YIDGKFVPSASGATFDTPNPAT-GETLMTLYEAQAADVDKAVKAARKAFDQGEWRTMSPA 81 YI+G+++ +A+ T ++ NPA E + T +QA D D+AV AAR+A+ G WR + Sbjct: 10 YINGQWLNAATETTLNSHNPANKSEIVATFPRSQADDTDRAVTAARQAY--GSWRKVPAP 67 Query: 82 SRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAIEHMRYYAGWCTKITGQ 141 +R+ ++++ +L+ +HK ELAQL + + GKPI E GD+ ++ Y AG ++ GQ Sbjct: 68 ARAEYIFRVGELLLQHKEELAQLISREMGKPITEA-RGDVQEGVDCAFYSAGEGRRLFGQ 126 Query: 142 TIPVSGAY-FNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAALATGCTIVLKPAEQTPLSA 200 T P F T P+GV I PWNFP+ + WK AL G T++LKPAE TP A Sbjct: 127 TTPSEMPNKFAMTVRMPIGVCALITPWNFPVAIPCWKAMPALVCGNTVILKPAEDTPACA 186 Query: 201 LYLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIAFTGSTEIGKKIMSTAAKSI 260 L E+ AG P GVIN++ G GE+AG+AL H +D ++FTGS+ G + T ++ Sbjct: 187 TKLIEIFAAAGLPPGVINLVHGVGEEAGKALVEHPNIDLVSFTGSSATGAYVGETCGRTH 246 Query: 261 KRVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQGQVCCAGSRVFIHKDQYDEVVDEM 320 KRV LE+GGK+ +++ DA+L+ A+ GAL G GQ C A SR+ +H+D ++ + Sbjct: 247 KRVCLEMGGKNAQVVMEDADLELALDGALWGAFGTTGQRCTATSRLILHRDIKEKFTTML 306 Query: 321 ASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDEGAKAVTGGSCPFEA----G 376 LR GAG +T IGP+++ Q +RV Y+ ++EGAK + GG E G Sbjct: 307 RERTSQLRLGAGTEPETDIGPIINNRQLQRVHEYMNIAREEGAKILIGGEIVTEGQLKQG 366 Query: 377 YFVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERANHSEYGLAAGLWTENVKQ 436 YF PT+ NV +M +A+EEIFGPV+ I T +E I N ++YGL++ ++T ++ + Sbjct: 367 YFFQPTILDNVTPQMRVAREEIFGPVVALIEVSTFEEAIAILNDTKYGLSSSVYTRDINR 426 Query: 437 AHYIADRLQAGTVWVNCYNV-FDAASPFGGYKQSGLG-REMGSYALDNYTEVKSVWVN 492 A ++ G ++N + + PFGG KQ+G G RE G+ ALD +TE KSV+V+ Sbjct: 427 AFVAMRDIEVGITYINGPTIGAEVHLPFGGVKQTGNGHREAGTTALDVFTEWKSVYVD 484 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: 597 Number of extensions: 29 Number of successful extensions: 7 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: 498 Length adjustment: 34 Effective length of query: 461 Effective length of database: 464 Effective search space: 213904 Effective search space used: 213904 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