Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_067911518.1 AQZ52_RS13160 betaine-aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_001519075.1:WP_067911518.1 Length = 469 Score = 348 bits (893), Expect = e-100 Identities = 188/466 (40%), Positives = 284/466 (60%), Gaps = 11/466 (2%) Query: 35 ETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKAVLNKLADLM 94 ETF+T++P T LA + ++D A++ A + +W+ + +R +L + ADL+ Sbjct: 3 ETFQTINPATGEVLATLPIAGKAEVDAAVAKAAAA--QKEWAKRTGTERGRILRRAADLL 60 Query: 95 EAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVATTSSHELAMIV 154 +ELA LET DTGKPI+ +L D+ A + ++A + GE Sbjct: 61 RERNDELAALETRDTGKPIQETLVVDVVSGADCLEFFAGIAPTIAGEHLDLGPAAFGYTR 120 Query: 155 REPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPD 214 REP+GV A I WN+P+ + CWK PALA GN++I KPSE +PL+AI + + +EAGLPD Sbjct: 121 REPLGVCAGIGAWNYPIQIACWKSAPALACGNAIIFKPSELTPLTAIEVEKIYREAGLPD 180 Query: 215 GVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSAN 274 G+ V+ GFG E G L+ H I I+ TGS TGK+++ A + +K V LE GGKS Sbjct: 181 GLFQVLHGFG-ETGALLTEHPGIAKISLTGSVPTGKRIMAGAA-ATLKNVTLELGGKSPL 238 Query: 275 IVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALLKQQAQNWQPGHP 334 I+FAD D++ A S FY+ G+VC GTR+ +E SI +FLA LK + + + G P Sbjct: 239 IIFADA-DIENAVSGAHLANFYSAGEVCSNGTRVFVERSILPQFLASLKARTERIKLGDP 297 Query: 335 LDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNA---GLAAA---IGPTIFVDVD 388 +DPAT MG+LI H + V +I G+++G +L G + G+ AA + PT+F Sbjct: 298 IDPATQMGSLISEGHLNKVMGYIETGKAEGAEVLTGGHRVTDGVPAAGFYVAPTVFTGCT 357 Query: 389 PNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHRMSRRLKAGS 448 + ++ REEIFGPV+ V F SE++ + AND+++GL A ++T+DL+RAHR+ L AGS Sbjct: 358 DDMTVVREEIFGPVMTVLPFDSEDEVIARANDTEFGLAAGIFTQDLTRAHRVIAALDAGS 417 Query: 449 VFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISLE 494 ++N +N + +PFGG+KQSG G + S A+ FT LK++++++E Sbjct: 418 CWINTFNICPVEMPFGGFKQSGLGFENSREAIHHFTRLKSVYVAME 463 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: 552 Number of extensions: 21 Number of successful extensions: 6 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: 469 Length adjustment: 34 Effective length of query: 461 Effective length of database: 435 Effective search space: 200535 Effective search space used: 200535 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