Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate AO356_28685 AO356_28685 betaine-aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28685 Length = 496 Score = 392 bits (1006), Expect = e-113 Identities = 220/486 (45%), Positives = 304/486 (62%), Gaps = 12/486 (2%) Query: 16 LAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDW 75 L+ RLFI G + AA F +P T+ LA++A G D+D A++AAR F G W Sbjct: 14 LSQPGRLFIGGTWQDAANGRRFAVENPATEHTLAEVAEGGERDVDAAVAAARAAFT-GTW 72 Query: 76 SLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAI 135 + SPA+R +L +LA+L++ H EELA L TL+ GKPI + R + AA IR++A Sbjct: 73 AQQSPAQRGLLLFRLAELLDQHREELAQLITLENGKPIG-AARGEAASAANIIRYFAGWP 131 Query: 136 DKVYGEVATTSSHE----LAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILK 191 K+ G S L +REPVGV A IVPWNFPL + WKLGP LA G +LK Sbjct: 132 TKIEGSTLPVSPSSGAPMLNYTLREPVGVCALIVPWNFPLTMCVWKLGPVLATGCVAVLK 191 Query: 192 PSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQ 251 P+E++PL AIRL L + AG P GV+N++TG G + G L++H D+D IAFTGST+ G+ Sbjct: 192 PAEQTPLVAIRLVQLIEAAGFPAGVVNLLTGLGAQTGAPLAQHPDVDKIAFTGSTQVGR- 250 Query: 252 LLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLE 311 L+ A NMK+V LE GGKS NI+ D D+ +AA A GIFYNQGQVC AG+RL + Sbjct: 251 LIAQAATGNMKKVSLELGGKSPNIILPDA-DIVRAAKGAADGIFYNQGQVCTAGSRLYVH 309 Query: 312 ESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDG- 370 S+ D+ L L++ A G LDPA++MG L+ +V +++ G+ +G L+ G Sbjct: 310 ASVLDQVLEELQRHAAAHVLGPGLDPASSMGPLVSARQLGTVRGYLQRGQEEGAELICGG 369 Query: 371 -RNAGLAAA--IGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGA 427 R A L I P++F+D A ++REEIFGPVL V +T ++ + ANDS YGL A Sbjct: 370 DRPAHLERGHFIRPSVFLDRAERACVAREEIFGPVLTVMSWTEIDELVLRANDSPYGLAA 429 Query: 428 AVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELK 487 +WTRDL AHR++ +LKAGSV++N +N D PFGGYKQSG GR+ + ++ +TE K Sbjct: 430 GLWTRDLRSAHRVAAQLKAGSVWINCWNVVDPASPFGGYKQSGWGREMGKNVIDAYTETK 489 Query: 488 TIWISL 493 ++++ L Sbjct: 490 SVYVDL 495 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: 647 Number of extensions: 32 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: 496 Length adjustment: 34 Effective length of query: 461 Effective length of database: 462 Effective search space: 212982 Effective search space used: 212982 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 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