Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate RR42_RS25005 RR42_RS25005 betaine-aldehyde dehydrogenase
Query= SwissProt::O34660 (495 letters) >FitnessBrowser__Cup4G11:RR42_RS25005 Length = 495 Score = 453 bits (1166), Expect = e-132 Identities = 236/500 (47%), Positives = 327/500 (65%), Gaps = 11/500 (2%) Query: 1 MSSLTMQVTKRLETFLQGTKKLYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVD 60 MSS T V + F+ GTK+L+I G +VP+ASG FDT NPATGE + L +A D+D Sbjct: 1 MSSTTYGV--QTPAFVGGTKRLFIGGAWVPAASGKAFDTVNPATGEVIARLAQADQTDID 58 Query: 61 KAVKAARKAFDQGEWRTMSPASRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGD 120 +AV AAR+AF+ G W + + R RL+ ++ D++E+H ELA +ETLD G P+ T G Sbjct: 59 RAVTAARQAFE-GPWNQWTHSDRQRLLIRIHDVVEKHFDELALIETLDMGAPLVRT-RGL 116 Query: 121 IPLAIEHMRYYAGWCTKITGQTIPVS---GAYFNYTRHEPVGVVGQIIPWNFPLLMAMWK 177 ++ + +YA T G P++ G + PVGVV IIPWN PLL W Sbjct: 117 KSFLLQLILFYASQ-TAAGGVQTPLNALPGKFATLKIKAPVGVVAGIIPWNGPLLSQWWI 175 Query: 178 MGAALATGCTIVLKPAEQTPLSALYLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAV 237 +GA LATGCT VLKPAE LSAL +AEL+ +AG PAGVIN++ G+G +AG AL H V Sbjct: 176 LGATLATGCTAVLKPAEDASLSALRMAELLQEAGVPAGVINVVTGYGGEAGSALAEHPGV 235 Query: 238 DKIAFTGSTEIGKKIMSTAAKSIKRVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQG 297 D+IAFTGS E G++I+ +A + KRV++ELGGKSP+I+ DANL KA+PG GV N G Sbjct: 236 DRIAFTGSPETGRRIVRASAGNFKRVSVELGGKSPDIVFDDANLDKAVPGVAMGVFTNTG 295 Query: 298 QVCCAGSRVFIHKDQYDEVVDEMASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQK 357 Q+C AG+RV + + YDE ++ + +++ SL+ G GL Q+GP+VS+ Q +RV+ Y+ Sbjct: 296 QICAAGTRVLVQRRIYDEFIERLKAFSTSLKIGNGLDPQVQLGPIVSQRQLDRVMHYVDV 355 Query: 358 GKDEGAKAVTGG---SCPFEAGYFVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEV 414 G EGA+ GG AGYFV PTVF V ++MTIA+EEIFGPV + +P++T ++ Sbjct: 356 GGQEGAELACGGRRLGGELAAGYFVEPTVFTGVHNDMTIAREEIFGPVASVMPFDTPEQA 415 Query: 415 IERANHSEYGLAAGLWTENVKQAHYIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGRE 474 + AN + +GLA G+WT+N+ AH A +QAGT+WVNCY V D FGGYK SG G + Sbjct: 416 LRIANDTSFGLAGGVWTQNLSTAHRFAQGIQAGTIWVNCYGVLDPQVGFGGYKLSGYGWK 475 Query: 475 MGSYALDNYTEVKSVWVNLE 494 + +D+Y K+V++NL+ Sbjct: 476 GAAEQVDSYLYQKAVYMNLD 495 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: 654 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: 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 Sep 17 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