Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_085219248.1 B9N75_RS13435 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_900177405.1:WP_085219248.1 Length = 498 Score = 218 bits (555), Expect = 4e-61 Identities = 155/463 (33%), Positives = 241/463 (52%), Gaps = 24/463 (5%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 FI+G A+ + + DP + A++ G + D+++AM AR + +W+ ++P + Sbjct: 7 FIDGGPHASGDRHG-DVFDPNSGQVQARVRLGTAADLEKAMERARAA--QPEWAATNPQR 63 Query: 83 RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142 R V+ K +L+EA+ E LA L + + GK I S + D+ I + + GE Sbjct: 64 RARVMFKFKELVEANMESLAALLSSEHGKVIADS-KGDVQRGLEVIEFACGIPHVLKGEY 122 Query: 143 ATTSSHELAMI-VREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAI 201 + + + +R+P+G++A I P+NFP ++ W G A+A GN+ ILKPSE+ P + Sbjct: 123 TQGAGPGIDVYSMRQPLGIVAGITPFNFPAMIPMWMFGVAIACGNAFILKPSERDPSVPV 182 Query: 202 RLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNM 261 RLA L KEAGLPDGVL VV G E A+ H+DI AI+F GS+ + G +N Sbjct: 183 RLAELMKEAGLPDGVLQVVHG-DKEMVDAILDHDDIKAISFVGSSDIA-HYIYSRGTANG 240 Query: 262 KRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLL-LEESIADEFLA 320 KRV G K+ IV D DL + A F + G+ C+A ++ + + A+ Sbjct: 241 KRVQAFGGAKNHGIVMPDA-DLDMVVNDLAGAAFGSAGERCMALPVVVPVGDKTANALRE 299 Query: 321 LLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIRE-GESKGQLLLDGRNAGLAA-- 377 L + + G D G ++ AH + V S+I+ + G+L++DGR L Sbjct: 300 KLVPAIEGLRVGVSTDAEAHYGPVVTQAHKEKVESYIQMCADEGGELVIDGRGFTLQGHE 359 Query: 378 ---AIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDL 434 +GPT F V P+ +EEIFGPVL + R S E A++L ++ QYG G A++TR+ Sbjct: 360 KGFFVGPTFFDHVKPSFRSYQEEIFGPVLQMVRAESFEDAVRLPSEHQYGNGVAIFTRNG 419 Query: 435 SRAHRMSRRLKAGSVFVNNYNDGDMTVP-----FGGYKQSGNG 472 A + R+ G V +N + VP FGG+K+SG G Sbjct: 420 HAAREFAARVNVGMVGIN----VPIPVPVAYHTFGGWKRSGFG 458 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: 565 Number of extensions: 43 Number of successful extensions: 4 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: 498 Length adjustment: 34 Effective length of query: 461 Effective length of database: 464 Effective search space: 213904 Effective search space used: 213904 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