Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate WP_075617845.1 GY23_RS03715 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
Query= SwissProt::O34660 (495 letters) >NCBI__GCF_001939075.1:WP_075617845.1 Length = 502 Score = 400 bits (1029), Expect = e-116 Identities = 206/477 (43%), Positives = 300/477 (62%), Gaps = 5/477 (1%) Query: 22 LYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKAARKAFDQGEWRTMSPA 81 LYI+G+F +A G T NP T E + + E QA D++KAV AAR+AFD+G W+TM A Sbjct: 20 LYINGEFTSAAGGTTMKNMNPFTNELINEVAEGQAEDINKAVAAAREAFDKGPWKTMKLA 79 Query: 82 SRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAIEHMRYYAGWC-TKITG 140 R +Y++ADL++E +A LE +D G PI++T + A E+ R+YA +++ G Sbjct: 80 KRMAYIYRIADLIDEEVERIAYLEAMDTGLPISQTKKM-VGRASENFRFYARMVESRLVG 138 Query: 141 QTIPVSGAYFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAALATGCTIVLKPAEQTPLSA 200 V + NYT + PVGV G I PWN P ++ WK+ ALATG T+VLKPAE +PLSA Sbjct: 139 DAYQVDDEFINYTINTPVGVAGLITPWNAPFMLETWKVAPALATGNTVVLKPAELSPLSA 198 Query: 201 LYLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIAFTGSTEIGKKIMSTAAKSI 260 LAE+I +A P GV N++ G GE AG+AL H V I+FTG T+ G I+ +A ++ Sbjct: 199 NLLAEIIHRADLPKGVFNVVHGVGETAGDALVKHPDVQLISFTGETKTGSTIIKNSADTL 258 Query: 261 KRVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQGQVCCAGSRVFIHKDQYDEVVDEM 320 K ++ELGGKSP I+ DA+ ++A+ + G+ G+ C A SR+F+ + D+ ++ + Sbjct: 259 KSCSMELGGKSPIIVFDDADFERALDACVWGIYSFNGERCTANSRLFLQETIKDQFIEAL 318 Query: 321 ASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDEGAKAVTGGSCPFE--AGYF 378 E ++ G L T++GPL+ K ++V SY+ K+EGA+ +T + P E G F Sbjct: 319 KERVEKIKIGDPLEAVTEVGPLIDKGHFQKVKSYLDIAKEEGAEVIT-ANIPDELTKGNF 377 Query: 379 VAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERANHSEYGLAAGLWTENVKQAH 438 VAPT+ N ++ M IA+EEIFGPVLT + ++ +E IE AN YGLA +WT ++K+ H Sbjct: 378 VAPTLLLNAKNHMRIAQEEIFGPVLTVMTFKDEEEAIELANDINYGLAGYVWTNDIKKGH 437 Query: 439 YIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGREMGSYALDNYTEVKSVWVNLED 495 +A R++AG +WVN NV D +PFGG K SG+GRE G Y + YTE K + V++ D Sbjct: 438 RVAHRVEAGMLWVNAQNVRDLRTPFGGSKYSGIGREGGHYGFEFYTEQKIIHVSISD 494 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: 614 Number of extensions: 28 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: 502 Length adjustment: 34 Effective length of query: 461 Effective length of database: 468 Effective search space: 215748 Effective search space used: 215748 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 Sep 24 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