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 3608018 Dshi_1425 aldehyde dehydrogenase (RefSeq)
Query= SwissProt::Q9DBF1 (539 letters) >FitnessBrowser__Dino:3608018 Length = 484 Score = 207 bits (528), Expect = 6e-58 Identities = 154/494 (31%), Positives = 231/494 (46%), Gaps = 28/494 (5%) Query: 38 QYAWLQDLGLREDNEGVY----NGSWGGRGEVITTYCPANNEPIARVRQASLKDYEETIG 93 Q + QD+ R D G Y NG+ + PA +E +A AS E+ I Sbjct: 4 QTGFAQDV--RVDFTGPYRHAINGALVDSAGSFEVFNPATDEVVAHAPNASRDQVEQAIA 61 Query: 94 KAKKAWNIWADIPAPKRGEIVRKIGDAFREKIQLLGRLVSLEMGKILVEGIGEVQEYVDV 153 AK A WA + +RG + DA Q L L++ E GK Sbjct: 62 AAKAAQPGWAALSQDERGAYIAAYADALDAHKQELITLLTTEQGK------PRHSMATTE 115 Query: 154 CDYAAGLSRMIGGPTLPSE----RPGHALIEMWNPLGLVGIITAFNFPVAVFGWNNAIAL 209 +YA R + L E P H + PLG+VG IT +NFPV + W A L Sbjct: 116 VEYAIFWVREVAKRRLEDEVIEDTPEHTVKVAHTPLGVVGAITPWNFPVLLGLWKIAPCL 175 Query: 210 ITGNVCLWKGAPTTSLVSVAVTKIIAQVLEDNLLPGAICSLVCGGADIGTTMARDERVNL 269 +TGN + K +P T L ++ +I QV P + ++V GG + G + + Sbjct: 176 VTGNTMVMKPSPYTPLCTLRFGEIAQQVF-----PAGVLNVVAGGNEQGAWLTEHPDIAK 230 Query: 270 LSFTGSTQVGKEVALMVQERFGKSLLELGGNNAIIAFEDADLSLVVPSVLFAAVGTAGQR 329 +SFTGST G++V + LELGGN+ I D ++P++ AA G +GQ Sbjct: 231 ISFTGSTATGRKVMASSSCNLKRITLELGGNDPAILLPGTDYKPLIPTLFDAAYGNSGQW 290 Query: 330 CTTVRRLFLHESIHNEVVDRLRSAYSQIRVGNPWDPNILYGPLHTKQAVSMFVRAVEEAK 389 C V+RL++HES++++ + + ++ VGN DPN GP+ K + K Sbjct: 291 CIAVKRLYVHESLYDDFLRDFVAHAAEKTVGNGMDPNTDLGPIQNKMQYGKLKDLFADVK 350 Query: 390 KQGGTVVYGGKVMDHPGNYVEPTIVTGLAHDAPIVHQETFAPILYVFKFQDEEEVFEWNN 449 QG +V GG++ D PGN+V TIV D+ +V +E F PIL + K+ D +EV N Sbjct: 351 AQGLSVPLGGEIPDGPGNFVPITIVDNPPKDSRVVREEPFGPILPIIKWSDLDEVVRDAN 410 Query: 450 EVKQGLSSSIFTKDLGRIFRWLGPKGS-DCGIVNVN-IPTSGAEIGGAFGGEKHTGGGRE 507 + + GL++S++ D +G + G V VN I G +I FGG K +G G E Sbjct: 411 DTEFGLAASVWGPDRDTA---IGVANRLEAGTVWVNEIHIHGIDI--PFGGHKQSGMGVE 465 Query: 508 SGSDAWKQYMRRST 521 +G + K++ T Sbjct: 466 NGQEGLKEFTNTKT 479 Lambda K H 0.319 0.137 0.421 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: 746 Number of extensions: 45 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: 539 Length of database: 484 Length adjustment: 35 Effective length of query: 504 Effective length of database: 449 Effective search space: 226296 Effective search space used: 226296 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 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