Align Alpha-aminoadipic semialdehyde dehydrogenase; Alpha-AASA dehydrogenase; Aldehyde dehydrogenase family 7 member A1; Antiquitin-1; Betaine aldehyde dehydrogenase; Delta1-piperideine-6-carboxylate dehydrogenase; P6c dehydrogenase; EC 1.2.1.31; EC 1.2.1.3; EC 1.2.1.8 (characterized)
to candidate WP_011765850.1 AZO_RS10715 aldehyde dehydrogenase
Query= SwissProt::Q64057 (539 letters) >NCBI__GCF_000061505.1:WP_011765850.1 Length = 501 Score = 462 bits (1190), Expect = e-134 Identities = 241/484 (49%), Positives = 320/484 (66%), Gaps = 10/484 (2%) Query: 60 GGRGEVITTYCPANNEPIARVRQASMKDYEETIGKAKKAWNIWADIPAPKRGEIVRKIGD 119 GG EV + P + +A++R AS ++ + IG+A +AW W IPAP RG +VR D Sbjct: 19 GGELEVRS---PIDGRTVAQLRPASHRETDAAIGRAHEAWLEWRTIPAPARGTLVRHYAD 75 Query: 120 ALREKIQLLGRLVSLEMGKILVEGIGEVQEYVDVCDYAAGLSRMIGGPTLPSERPGHALM 179 ALR L L++LE GKI E +GEVQE +D+CD+AAGLSR + G T+ SERPGH L Sbjct: 76 ALRRHKTALAELITLESGKIRQESLGEVQEMIDICDFAAGLSRQLHGLTIASERPGHRLQ 135 Query: 180 EQWNPLGLVGIITAFNFPVAVFGWNNAIALITGNVCLWKGAPTTSLVSIAVTKIIAKVLE 239 E W+P G+VG+I+AFNFP AV+ WN A+A + G+ +WK +P T L ++A + Sbjct: 136 ELWHPAGVVGVISAFNFPAAVWAWNAALAWVCGDTVIWKPSPRTPLTALACASLFNDACA 195 Query: 240 DNLLP-GAICSLTCGGADMGTAMARDERVNLLSFTGSTQVGKQVALMVQERFGKSLLELG 298 + + + GG + +A D RV +LS TGST +G+++A +V RFG+S+LELG Sbjct: 196 THSQGCEGLLEVLIGGNEPARQLAADRRVAVLSATGSTAMGREIAPVVASRFGRSILELG 255 Query: 299 GNNAIIAFEDADLSLVLPSALFAAVGTAGQRCTTVRRLFLHESIHDEVVDRLKNAYSQIR 358 GNNA I ADL L + LFAA GTAGQRCTT+RRL +HE IHD ++ RL+ A++Q+R Sbjct: 256 GNNAAIVTPSADLDLTERAVLFAAAGTAGQRCTTLRRLIVHEHIHDTLLARLQAAWAQLR 315 Query: 359 VGNPWDPNILYGPLHTKQAVSMFVQAVEEAKKEGGTVVYGGKVMDHP----GNYVEPTIV 414 +GNP +P++L GPL A A+ EA+ EGG V+GG+ P G Y P +V Sbjct: 316 IGNPMEPDVLVGPLIEASAGEAMTAALAEAEAEGGR-VFGGEAYPVPGLGSGCYRRPALV 374 Query: 415 TGLVHDAPIVHKETFAPILYVFKFKNEEEVFEWNNEVKQGLSSSIFTKDLGRIFRWLGPK 474 + P+V +ETFAPILYV +++ E+ NN V QGL+S+IFT+DLG ++ Sbjct: 375 -AMPAQTPVVMRETFAPILYVLRYRTLEDAIAMNNAVPQGLASAIFTRDLGEAEAFISAS 433 Query: 475 GSDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYMRRSTCTINYSTALPLAQ 534 GSDCGIVNVN SGAEIGGAFGGEK TGGGRE+GSD WK YMRR+TCTIN S +LPLAQ Sbjct: 434 GSDCGIVNVNTGPSGAEIGGAFGGEKDTGGGREAGSDVWKTYMRRATCTINGSGSLPLAQ 493 Query: 535 GIKF 538 GI+F Sbjct: 494 GIRF 497 Lambda K H 0.319 0.137 0.417 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: 834 Number of extensions: 33 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: 539 Length of database: 501 Length adjustment: 35 Effective length of query: 504 Effective length of database: 466 Effective search space: 234864 Effective search space used: 234864 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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