Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate WP_075617829.1 GY23_RS03610 aldehyde dehydrogenase
Query= SwissProt::O34660 (495 letters) >NCBI__GCF_001939075.1:WP_075617829.1 Length = 505 Score = 412 bits (1058), Expect = e-119 Identities = 207/472 (43%), Positives = 301/472 (63%), Gaps = 5/472 (1%) Query: 22 LYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKAARKAFDQGEWRTMSPA 81 L I+G+ V S++G T T NPATGE + + +A D +KAV+AAR +FD G+W+ Sbjct: 21 LIINGEKVKSSTGETIKTFNPATGELIAEVAKASKEDAEKAVEAARNSFDHGKWKLYPIG 80 Query: 82 SRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAIEHMRYYAGWCTKITGQ 141 RS+ + K+A +M EL +LE LD GK ++ G + AIE +YAG G Sbjct: 81 RRSQTLNKIAAIMRARFNELVELEILDTGKSLH-AAQGQVSQAIEDFEFYAGAIVGHRGS 139 Query: 142 TIPVSGAYFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAALATGCTIVLKPAEQTPLSAL 201 V G + NYT EPVGV QIIPWN+PL+MA WK+ A+A GC++++KPA TPL+A+ Sbjct: 140 VNNVPGQFHNYTEIEPVGVCAQIIPWNYPLMMAAWKIAPAIAVGCSVIVKPASLTPLTAI 199 Query: 202 YLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIAFTGSTEIGKKIMSTAAKSIK 261 L E+ +AG PAGV+N+IPG G D G L H V+K+AFTGST IGK IM+ A++++K Sbjct: 200 ILGEICLEAGVPAGVVNVIPGNGADVGNFLVEHPRVNKVAFTGSTPIGKDIMAKASQTLK 259 Query: 262 RVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQGQVCCAGSRVFIHKDQYDEVVDEMA 321 RVTLELGGKSP+++ DA++ A+ G+L G+ +N GQ C A SR+++H+D YDE +++ Sbjct: 260 RVTLELGGKSPSLVFEDADIDAAVDGSLFGIFYNSGQSCEARSRLYVHEDIYDEFMNKFI 319 Query: 322 SYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDEGAKAVTGGSCP----FEAGY 377 + L+ G +K T +G ++ + Q + + SY+Q K+EGA + GG +E G+ Sbjct: 320 EKTKKLQLGNPFNKGTHVGAIIDQGQLDTIDSYVQSAKNEGADILVGGKIAKLEGYENGF 379 Query: 378 FVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERANHSEYGLAAGLWTENVKQA 437 + PT+ ANV M +EIFGPV+ + ++ E I AN SE+GL + +W+++ +A Sbjct: 380 WYEPTIIANVTHSMKAVTDEIFGPVVVVMKFKDEKEAIRLANDSEFGLGSAVWSKDGARA 439 Query: 438 HYIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGREMGSYALDNYTEVKSV 489 +A+++QAG V VNC +PFGGYKQSG GRE+ LD YTE KS+ Sbjct: 440 TRVANQIQAGIVMVNCPFSAFPGTPFGGYKQSGFGRELCIETLDLYTETKSI 491 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: 649 Number of extensions: 35 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: 505 Length adjustment: 34 Effective length of query: 461 Effective length of database: 471 Effective search space: 217131 Effective search space used: 217131 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