Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_104913707.1 C3B54_RS06115 gamma-aminobutyraldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_002950575.1:WP_104913707.1 Length = 478 Score = 292 bits (747), Expect = 2e-83 Identities = 178/470 (37%), Positives = 265/470 (56%), Gaps = 9/470 (1%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 FING+Y + +ET VDP T+ A + D+D A AA FE WS ++PA+ Sbjct: 9 FINGQYVDSKGSETIPLVDPATEEVYAHSPISSAADVDDAYQAASKAFE--GWSETTPAE 66 Query: 83 RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142 R+ L ++AD +E EE A LE+ D GKP + D+I + IR++A A + G+ Sbjct: 67 RQLALFRIADELEKRGEEFADLESQDAGKPRASLVEDEISLSVDQIRFFAGAARNLEGKS 126 Query: 143 ATTSSHE-LAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAI 201 A + + I REP+GV+ + PWN+PL + WK PA+AAGN+ +LKPS+ +P S + Sbjct: 127 AGEYMKDHTSFIRREPIGVVGQVAPWNYPLNMAVWKFAPAVAAGNTTVLKPSDTTPQSTL 186 Query: 202 RLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNM 261 LA + LP+GV+NV+TG G A+ H + ++ TGS R G ++ K A +++ Sbjct: 187 LLAEICA-MHLPEGVVNVITG-DRTTGGAMIDHKIPEMVSITGSVRAGLEVAKAAA-TDL 243 Query: 262 KRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLAL 321 KRV LE GGK+ IVF D D+ A ++N GQ C A TR+++ ESI DEF+A Sbjct: 244 KRVHLELGGKAPVIVFDDA-DIPSAIEGIGIAGYFNAGQDCTAATRVVVHESIHDEFIAE 302 Query: 322 LKQQ-AQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDG-RNAGLAAAI 379 LK+ A N G P DP T G + + D V + E S + G R I Sbjct: 303 LKKWVAANVTTGLPSDPNTFYGPVNNANQMDRVMGILGELPSHSTVEAGGVRQGERGYFI 362 Query: 380 GPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHR 439 PTI + N + + EIFGPV+ V F +EE+A+ +AN YGL ++VWT+D +RA R Sbjct: 363 EPTIVSGLKQNDAAIQTEIFGPVITVQPFRTEEEAMTMANGVPYGLSSSVWTKDHARAMR 422 Query: 440 MSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTI 489 ++ L G+V++N + +P GG+K SG+G+D S + E++T +K + Sbjct: 423 FAKGLDFGAVWINCHIPLVAEMPHGGFKHSGHGKDLSQYGFEEYTRVKHV 472 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: 564 Number of extensions: 29 Number of successful extensions: 8 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: 478 Length adjustment: 34 Effective length of query: 461 Effective length of database: 444 Effective search space: 204684 Effective search space used: 204684 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