Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_017221244.1 A923_RS0108515 betaine-aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_000276805.1:WP_017221244.1 Length = 487 Score = 310 bits (795), Expect = 6e-89 Identities = 176/479 (36%), Positives = 271/479 (56%), Gaps = 13/479 (2%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 +++G+ A ETFE ++P T A + + A+ +A+ F WS +P + Sbjct: 9 YVHGQSIANETGETFEVINPATGAVSYLVEVADASVQQAAIDSAKAGFST--WSKMTPME 66 Query: 83 RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142 R +L K L+ +ELA +E DTGKP + + D+ A +I ++A + G Sbjct: 67 RSRILLKAVALLRERNDELAAIEVQDTGKPWQEASVVDVVTGADSIEFFAGLAPSIEGNQ 126 Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202 + REP+G+ A I WN+PL + CWK PALA GN +I KPSE++P AI+ Sbjct: 127 QQVGD-DFYYTRREPLGICAGIGAWNYPLQIACWKAAPALACGNVMIFKPSEETPRGAIK 185 Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262 LA + +AG+P GV NVV G G G L+ H +I ++FTG TGK+++ A S +K Sbjct: 186 LAEVFTDAGVPHGVFNVVQGDGR-VGAWLTTHEEIAKVSFTGEVGTGKKVMAAAAGS-LK 243 Query: 263 RVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALL 322 +V +E GGKS I+F D D+ A SA FY QG+VC GTR+ ++++I F+ L Sbjct: 244 QVTMELGGKSPLIIFDDA-DVDNAVSAAMLANFYTQGEVCTNGTRVFVQDAIYPRFIEKL 302 Query: 323 KQQAQN-WQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGR------NAGL 375 +Q+ +N G P+DP T G LI H V +FI G+++G LL G NA Sbjct: 303 RQRTENNIICGDPMDPETNFGALISKDHQQKVLNFIEIGKAEGAELLTGGHALKPDNAPN 362 Query: 376 AAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLS 435 + PTIF +LS+EEIFGPV+ V F+ E++ ++ AND++ GL A V+T+D++ Sbjct: 363 GYFVAPTIFTQCTDEMTLSKEEIFGPVMSVLTFSDEDEVVRRANDTRLGLAAGVFTQDIT 422 Query: 436 RAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISLE 494 RAHR+ +++AG ++N Y +P GGYK SG GR+ L+ +T++K +++ ++ Sbjct: 423 RAHRVIHQMEAGICWINAYGASPAEMPVGGYKMSGIGRENGSETLKAYTQIKAVYVGMQ 481 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: 571 Number of extensions: 30 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: 487 Length adjustment: 34 Effective length of query: 461 Effective length of database: 453 Effective search space: 208833 Effective search space used: 208833 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