Align Putative aldehyde dehydrogenase transmembrane protein; EC 1.2.1.3 (characterized, see rationale)
to candidate WP_074201782.1 BUQ81_RS07630 NAD-dependent succinate-semialdehyde dehydrogenase
Query= uniprot:Q92L07 (510 letters) >NCBI__GCF_900141795.1:WP_074201782.1 Length = 458 Score = 177 bits (448), Expect = 9e-49 Identities = 136/445 (30%), Positives = 204/445 (45%), Gaps = 14/445 (3%) Query: 35 SFSPVTGEKIASLKTVSAAEAAGKIEKADEAFRAW-RLVPAPKRGELVRLLGEELRAFKA 93 S +P T E+ A + + + A A R W + P R EL+R + E LR K Sbjct: 7 SINPATEEENARIPVWDDDKLDTALRYAGYAQRDWAQQTPLETRCELLRNVAELLRVKKR 66 Query: 94 DLGRLVSIEAGKIPSEGLGEVQEMIDICDFAVGLSRQLYGLTIATERPGHRMMETWHPLG 153 +L L + E GK E EV++ +CDF + + + E R + + PLG Sbjct: 67 ELAELATREMGKRIGEAEAEVEKCAWVCDFYADQAPAMLADEVV-ETEATRSLVVYQPLG 125 Query: 154 VVGIISAFNFPVAVWSWNAALALVCGDAVVWKPSEKTPLTALACQAILERAIARFGDAPE 213 V+ + +NFP AA ALV G+ VV K + PL ALA + + + A PE Sbjct: 126 VILAVMPWNFPYWQVFRAAAPALVAGNGVVLKHASNVPLCALAIEGLFKEA-----GFPE 180 Query: 214 GLSQVLIGDRAIGEVLVDHPKVPLVSATGSTRMGREVGPRLAKRFARAILELGGNNAGIV 273 L Q L+ A E + HP V V+ TGS GR V + + +LELGG++ ++ Sbjct: 181 DLFQSLMITSAQVERAICHPDVRGVTLTGSEPAGRAVASIAGRELKKTVLELGGSDPFVI 240 Query: 274 CPSADLDMALRAIAFGAMGTAGQRCTTLRRLFVHESVYDQLVPRLKKAYQSVSV-GNPLE 332 P ADLD + GQ C +R V ++++D+ V R K A + V G+P++ Sbjct: 241 LPDADLDEVVPMALKARFINMGQSCIAAKRFLVDKTMHDEFVARFKVAIEDYFVPGDPMD 300 Query: 333 SAALVGPLVDKAAFDGMQKAIAEAKNHGGAV-TGGERVELGHENGYYVKPALVEMPKQEG 391 A +GP+ + + + + A+++G V TGG+ L YY L + Sbjct: 301 PATTLGPMARRDLMEELHNQVIRAQDYGATVETGGQ--TLDRPGAYYAPTLLTNVTTSNP 358 Query: 392 PVLEETFAPILYVMKYSDFDAVLAEHNAVAAGLSSSIFTRDMQESERFLAADGSDCGIAN 451 EE F P+ V Y++ L NA GL S++T D+ E A G CG A Sbjct: 359 AFQEELFGPVATVTTYTEPSHALGLANATRFGLGGSVWTTDIATGEAI--ARGMQCGCAF 416 Query: 452 VNIGTSGAEIGGAFGGEKETGGGRE 476 VN ++ FGG K++G GRE Sbjct: 417 VN-DMVRSDPRLPFGGIKDSGYGRE 440 Lambda K H 0.317 0.134 0.390 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: 489 Number of extensions: 21 Number of successful extensions: 6 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: 510 Length of database: 458 Length adjustment: 34 Effective length of query: 476 Effective length of database: 424 Effective search space: 201824 Effective search space used: 201824 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 (21.7 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