Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate WP_033100857.1 JG50_RS0109305 aldehyde dehydrogenase
Query= SwissProt::O34660 (495 letters) >NCBI__GCF_000763315.1:WP_033100857.1 Length = 499 Score = 419 bits (1078), Expect = e-122 Identities = 212/474 (44%), Positives = 305/474 (64%), Gaps = 9/474 (1%) Query: 22 LYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKAARKAFDQGEWRTMSPA 81 L I G+ VPS SG F NPA GE + + +A ADVD+AV++AR A +W + Sbjct: 15 LLIGGEHVPSESGEYFTVYNPANGEAIAQVAKATRADVDRAVQSARDALSNSKWARWPAS 74 Query: 82 SRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAIEHMRYYAGWCTKITGQ 141 R +++ K+A +M + +L +LE L++GK ++ G + AIE YAG T I G Sbjct: 75 RRGQILNKIASIMRQRFNDLVELEVLNSGKALS-AAKGQVMQAIEDFELYAGAVTTIQGH 133 Query: 142 TIPVSGAYFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAALATGCTIVLKPAEQTPLSAL 201 T PV +F+Y+ EPVGV QI+PWN+PL+M WK+ ALA GCT++LKPA TPL+AL Sbjct: 134 TKPVPNGFFHYSVKEPVGVCAQIVPWNYPLMMTAWKVAPALAAGCTLILKPASLTPLTAL 193 Query: 202 YLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIAFTGSTEIGKKIMSTAAKSIK 261 LA++ +AG PAGVIN+I G G D G L H VDK+AFTG T GK IM+ A+ ++K Sbjct: 194 VLADICHEAGVPAGVINVITGSGADVGSYLVEHPGVDKVAFTGETTTGKDIMAKASDTLK 253 Query: 262 RVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQGQVCCAGSRVFIHKDQYDEVVDEMA 321 RVTLELGGKSPNI+ DA+L+ A+ G++ G+ +N GQ C A SR+F+H+D YD +++ Sbjct: 254 RVTLELGGKSPNIVFADADLEAAVNGSVYGIYYNTGQSCEARSRLFVHEDIYDAFIEKFV 313 Query: 322 SYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDEGAKAVTGGSCP----FEAGY 377 + L+ G +++T +G ++S+ Q + + SY++ + EGA+ + GG P F GY Sbjct: 314 EQTKKLKLGDPFNEETHVGAVISQGQWDTIDSYVKLAEKEGARVLYGGKRPEGEEFAKGY 373 Query: 378 FVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERANHSEYGLAAGLWTENVKQA 437 + PTV + ++M +A+EEIFGPV+ I ++ EV++ AN + YGLAA +WT + +A Sbjct: 374 WYMPTVIVDATNDMRVAQEEIFGPVVVVIKFKDEKEVVKLANETMYGLAAAVWTRDFGRA 433 Query: 438 HYIADRLQAGTVWVNCYNVFDA--ASPFGGYKQSGLGREMGSYALDNYTEVKSV 489 H +A +L+AG V +N N F A PFGGYKQSG GRE+ +L+ Y E KSV Sbjct: 434 HRVASQLKAGVVMIN--NPFSAFPGLPFGGYKQSGFGRELAIESLELYMETKSV 485 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: 640 Number of extensions: 25 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: 495 Length of database: 499 Length adjustment: 34 Effective length of query: 461 Effective length of database: 465 Effective search space: 214365 Effective search space used: 214365 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