Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate WP_011842150.1 RSPH17029_RS16005 aldehyde dehydrogenase
Query= SwissProt::O34660 (495 letters) >NCBI__GCF_000015985.1:WP_011842150.1 Length = 495 Score = 417 bits (1073), Expect = e-121 Identities = 213/472 (45%), Positives = 306/472 (64%), Gaps = 4/472 (0%) Query: 23 YIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKAARKAFDQGEWRTMSPAS 82 +IDG++V S SG TF P G L + AADVD AV++AR+AF+ G W M+PA Sbjct: 21 FIDGQYVDSLSGETFACIYPGDGRPLTDVASCNAADVDVAVRSARRAFEAGVWSRMAPAD 80 Query: 83 RSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAIEHMRYYAGWCTKITGQT 142 R R++ + ++L+ ++ ELA LETL+ GKPI NGD+ A + +YA K+ G+ Sbjct: 81 RRRILLRFSELILANREELALLETLNVGKPIANAYNGDVVSAAACIAWYAEAIDKVYGEV 140 Query: 143 IPVSGAYFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAALATGCTIVLKPAEQTPLSALY 202 + EP+G+V ++PWN+P+ MA WK+G ALATG +++LKPAEQ+P +AL Sbjct: 141 AATAHDMTTLVMREPLGIVAAVVPWNYPMSMAAWKLGPALATGNSVILKPAEQSPFTALK 200 Query: 203 LAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIAFTGSTEIGKKIMSTAAKS-IK 261 EL +AG P GV+N++PG G AG+AL H VD + FTGSTE+GK M + +S IK Sbjct: 201 FGELAIEAGMPPGVLNVVPGLGHIAGKALGLHMDVDCVGFTGSTEVGKYFMQYSGQSNIK 260 Query: 262 RVTLELGGKSPNILLPDA-NLKKAIPGALNGVMFNQGQVCCAGSRVFIHKDQYDEVVDEM 320 R+ LELGGKSP ++L D +L A G G+ N GQVC AGSR+ + + +D++++++ Sbjct: 261 RIGLELGGKSPQVVLADCDDLDAAAAGIAAGIFANTGQVCNAGSRLIVDEKIHDQLLEKI 320 Query: 321 ASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDEGAKAVTGGS--CPFEAGYF 378 A+ A+ G L T++G +VS+EQ +RVL YI G+ +GA+ V GG G++ Sbjct: 321 AAQAKVFAPGDPLDTATRMGSMVSEEQMDRVLGYIDAGRADGARPVIGGGRVKTETGGFY 380 Query: 379 VAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERANHSEYGLAAGLWTENVKQAH 438 + PT+F V ++M IA+EEIFGPVL+AIP + DE + AN + YGLA +WT +VK AH Sbjct: 381 IEPTIFEGVRNDMKIAQEEIFGPVLSAIPVKGFDEAMAVANDTVYGLAGAVWTGSVKNAH 440 Query: 439 YIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGREMGSYALDNYTEVKSVW 490 A L+AG VWVNC++ A PFGG+KQSG GR+ +A+D YT++K+VW Sbjct: 441 RAAKSLRAGVVWVNCFDRGSLAVPFGGFKQSGFGRDKSLHAMDKYTDLKAVW 492 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: 619 Number of extensions: 29 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: 495 Length adjustment: 34 Effective length of query: 461 Effective length of database: 461 Effective search space: 212521 Effective search space used: 212521 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 10 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