Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_036264374.1 DL86_RS17780 bifunctional proline dehydrogenase/L-glutamate gamma-semialdehyde dehydrogenase PutA
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_000746085.1:WP_036264374.1 Length = 1033 Score = 154 bits (389), Expect = 1e-41 Identities = 142/481 (29%), Positives = 221/481 (45%), Gaps = 24/481 (4%) Query: 30 AAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKAVLNK 89 AA E P+ + + + + AM ARG F+ WS + R A L++ Sbjct: 550 AAREGAARAIASPIDGSSIGLVREAAPGLLQEAMREARGGFKI--WSRTPVGLRAACLDR 607 Query: 90 LADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAI---RWYAEAIDKVYGEVATTS 146 A +EA A L ++ GK +L D I AI R+YA+ + + A Sbjct: 608 AAQELEAQAPRWLHLLQIEAGK----TLEDAIGEWREAIDFCRYYAQEARRRFASPAPMP 663 Query: 147 --SHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLA 204 + E + GV I PWNFPL + ++ ALAAGNSV+ KP+E++PL A + Sbjct: 664 GPTGEDNRLFCHGRGVFVCISPWNFPLSIFLGQIAAALAAGNSVLAKPAEQTPLIAAQAV 723 Query: 205 GLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKD--AGDSNMK 262 L AG+P VL+++ G G + G AL + + +A TGS T ++ + A + Sbjct: 724 SLLYRAGVPASVLHLLPGDG-DVGAALVALDGVAGVAITGSMDTATKINRSLAAKSGPIA 782 Query: 263 RVWLEAGGKSANIVFADCPDL-QQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLAL 321 ++ E GG N + AD L +Q A F + GQ C A L L+E +AD +A+ Sbjct: 783 QLIAETGG--VNAMIADATALPEQVCDDVVASAFRSAGQRCSALRLLCLQEDVADRMIAM 840 Query: 322 LKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAAIGP 381 +K A+ G P +G +ID A S+ + I + + + GR A G Sbjct: 841 IKGAARELLVGDPRALGVHVGPVIDLAAKRSLEAHIEDMRACAIVHYAGRAPSTAPPRGF 900 Query: 382 TIFVDVDPNASLS--REEIFGPVLVVTRFTSEEQA--LQLANDSQYGLGAAVWTRDLSRA 437 + + +S+S R E FGP+L V R+ + E L + +GL V +R + Sbjct: 901 YLAPHIFELSSVSDLRREAFGPILHVARYKASELGGLLDSIEAAGFGLTLGVHSRIDAVI 960 Query: 438 HRMSRRLKAGSVFVNNYNDGDM--TVPFGGYKQSGNG-RDKSLHALEKFTELKTIWISLE 494 + R AG+ +VN G + T PFGG+ SG G + H L++F +T+ I+ Sbjct: 961 DEIVERRLAGNCYVNRNMIGAVVGTQPFGGFGLSGTGPKAGGPHYLDRFCVEQTVTINTA 1020 Query: 495 A 495 A Sbjct: 1021 A 1021 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: 961 Number of extensions: 41 Number of successful extensions: 5 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: 1033 Length adjustment: 39 Effective length of query: 456 Effective length of database: 994 Effective search space: 453264 Effective search space used: 453264 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: 55 (25.8 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