Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate H281DRAFT_00993 H281DRAFT_00993 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Burk376:H281DRAFT_00993 Length = 497 Score = 464 bits (1194), Expect = e-135 Identities = 231/490 (47%), Positives = 336/490 (68%), Gaps = 5/490 (1%) Query: 9 WQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARG 68 W+ KA +L+++ R FI G+ AA NETF T++P T LA IA+ + D+DRA++AAR Sbjct: 7 WKQKADALSLDGRAFIAGQRANAASNETFATLNPSTGKVLADIAKCDTKDVDRAVAAARE 66 Query: 69 VFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAI 128 FE G WS ++PA+RKAVL +LA L++ +AEELALLE L+ GKPI L DIP +A I Sbjct: 67 AFESGVWSKAAPAQRKAVLQRLAQLIDDNAEELALLEALEAGKPISECLGLDIPESAACI 126 Query: 129 RWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSV 188 RW+AE DK Y ++ + + ++MI REP+GV+ A++PWNFP L+ WK+GPAL+ GNSV Sbjct: 127 RWHAEVTDKRYDALSPSGASVVSMITREPIGVVGAVLPWNFPALMLAWKIGPALSVGNSV 186 Query: 189 ILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRT 248 I+KP+E++ LS +R+A LA EAGLP GVLNVVTGFG AGQAL RH D+D +AFTGST T Sbjct: 187 IVKPAEQTSLSTLRIADLALEAGLPAGVLNVVTGFGESAGQALGRHADVDLVAFTGSTET 246 Query: 249 GKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRL 308 GK+ L+ + D+N+KRV LE GGK+ +V D +L A A F+N G+ C AG+R+ Sbjct: 247 GKRFLRYSADTNLKRVVLECGGKNPQVVLPDVANLDAVAEQAVAAAFWNMGENCSAGSRI 306 Query: 309 LLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLL 368 L+ S+ L + + W+ G PLDP +G+LI+ H + V + I + ++G L+ Sbjct: 307 LVPSSLKASLLEKVLAVLEVWKTGDPLDPDVKLGSLIEEMHFEKVLAHIEKARAEGARLV 366 Query: 369 DGRNAGLAAAIG----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYG 424 G A + G PTIF +V P ++R+E+FGPV+ + ++A+ +AND+ YG Sbjct: 367 CGGKATRTDSGGWFVEPTIFDNVTPQMRIARDEVFGPVVCFIEYADIDEAVHIANDTCYG 426 Query: 425 LGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSG-NGRDKSLHALEKF 483 L A++WT +++ AH+++ R++AG+V VN + +GD++ PFGG+KQSG GRDKS++A +++ Sbjct: 427 LAASLWTDNVNHAHKIAARIRAGTVTVNCFGEGDLSTPFGGFKQSGFGGRDKSVYAHDQY 486 Query: 484 TELKTIWISL 493 ELKT W+ L Sbjct: 487 CELKTTWLKL 496 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: 600 Number of extensions: 27 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: 495 Length of database: 497 Length adjustment: 34 Effective length of query: 461 Effective length of database: 463 Effective search space: 213443 Effective search space used: 213443 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