Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_092346115.1 BLU87_RS07020 aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_900107645.1:WP_092346115.1 Length = 491 Score = 359 bits (922), Expect = e-103 Identities = 193/479 (40%), Positives = 286/479 (59%), Gaps = 11/479 (2%) Query: 21 RLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSP 80 +L+I+G++ A++ +TFE P LA A D+D A+ AA F +W SP Sbjct: 10 KLYIDGKWVDASDGKTFEAHCPADGKLLATCANATKQDVDDAVKAAWKAFP--EWKDISP 67 Query: 81 AKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYG 140 R +L K+ADL++ +AE+LA++E++D GKP+R + D+P A+ R++A I G Sbjct: 68 QDRSIILLKIADLIDENAEKLAMIESIDNGKPLRETTAVDVPLASDHFRYFAGVIRAQEG 127 Query: 141 EVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSA 200 + + +++I+REP+GVI I+PWNFPLL+ WK+ PALAAGN V+LKPS + LS Sbjct: 128 QAVMIDKNTMSIILREPIGVIGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPSSTTSLSL 187 Query: 201 IRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSN 260 + A L + LP GV+NVVTG G G + H +AFTGST G + DA Sbjct: 188 LEFAKLL-DTVLPPGVVNVVTGKGSSTGNFVLEHEGFSKLAFTGSTEVGYN-IADAAAKK 245 Query: 261 MKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLA 320 + LE GGKSANI F DCP ++A T GI NQGQVC AG+R+ ++ESI D+F+ Sbjct: 246 LIPATLELGGKSANIYFEDCP-WEKAIEGTQLGILLNQGQVCCAGSRVFVQESIYDKFVE 304 Query: 321 LLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAAIG 380 + + + + P T MG ID + + +++ G+ +G L+ G +G Sbjct: 305 AMAEAFKKVKVNLPWADGTMMGAQIDEVQLNKILAYVEVGKQEGARLVTGGKRITTGELG 364 Query: 381 ------PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDL 434 PT+F DV+ + +++EEIFGPV+ V +F EE+ + +ANDS YGL AVWT+D+ Sbjct: 365 KGYFMEPTLFADVNNDMRIAQEEIFGPVVCVIKFKDEEEVINMANDSDYGLAGAVWTKDI 424 Query: 435 SRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISL 493 +RA R++R ++ G ++VN YN PFGGYK+SG GR+ LE +T+ K I+IS+ Sbjct: 425 NRALRVARAVQTGRMWVNTYNQLPAHTPFGGYKKSGIGRETHKMMLEHYTQTKNIYISM 483 Lambda K H 0.317 0.133 0.389 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: 542 Number of extensions: 22 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: 495 Length of database: 491 Length adjustment: 34 Effective length of query: 461 Effective length of database: 457 Effective search space: 210677 Effective search space used: 210677 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