Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_086509897.1 BZY95_RS10630 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_002151265.1:WP_086509897.1 Length = 489 Score = 365 bits (937), Expect = e-105 Identities = 198/478 (41%), Positives = 286/478 (59%), Gaps = 8/478 (1%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 +I+G A SGETF+ L+P DG LA+V AD +RAV A A+ W+ + + Sbjct: 10 YIDGRREPATSGETFDVLNPYDGSLLARVDQASQADIDRAV--ASASQGQRRWAAMTGMQ 67 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R L R LLR+ +ELA LET + GKPI +++++DI A + + A + Sbjct: 68 RGRVLQRAVALLRERNDELAELETRNTGKPISETAAVDIVTGADVLEYYAGLAPAIEGAQ 127 Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 P REP+GV+ AI WN+P+ +ACWK PALA GN+VV KPSE +PLTA++ Sbjct: 128 IPLRESSFVYTRREPLGVIAAIGAWNYPIQIACWKAAPALAAGNAVVFKPSEVTPLTAMK 187 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 +A++ E G+P GV NV+ G VG+ L H + + FTG K++M AG S +K Sbjct: 188 LAEIFTEVGLPDGVFNVVHGEAR-VGQMLTAHEGIAKVSFTGEVGTGKKVMAAAGGSTLK 246 Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMV 322 + +E GGKSP IVFADA DL AA+AA A ++ G++CT G+R+ VERS+K F + Sbjct: 247 DVTMELGGKSPLIVFADA-DLDRAADAAMMANFYSSGQICTNGTRVFVERSVKAAFEEKI 305 Query: 323 VEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE---TG 379 VE + + G+PLDP+ G LV + VL YI G +DGA++L GG+ L+E Sbjct: 306 VERVARIRAGDPLDPEINFGPLVSFEHQAKVLDYIAYGKQDGARVLIGGE-PLDEGDFAR 364 Query: 380 GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDIS 439 G + T+F ++ MRI +EEIFGPV+S++ FD EE + ANDT YGLAAG++T ++ Sbjct: 365 GAWAPATVFTDCSDEMRIVREEIFGPVMSILVFDDEEELIRRANDTHYGLAAGVFTESLA 424 Query: 440 KAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497 +AH+T + AG W+N + P GG+KQSG GR+ + L YT+ K+ +++ Sbjct: 425 RAHRTIHRMEAGICWINTWGESPAEMPVGGYKQSGVGRENGIETLAHYTQTKSVQVEM 482 Lambda K H 0.316 0.132 0.390 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: 610 Number of extensions: 26 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: 497 Length of database: 489 Length adjustment: 34 Effective length of query: 463 Effective length of database: 455 Effective search space: 210665 Effective search space used: 210665 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 (21.6 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