Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_090445819.1 BLS63_RS14555 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_900100495.1:WP_090445819.1 Length = 490 Score = 372 bits (954), Expect = e-107 Identities = 195/481 (40%), Positives = 286/481 (59%), Gaps = 5/481 (1%) Query: 19 EGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQL 78 E + +I G Y A SG +FE ++P G LA+V AD RAV +A A VW+ + Sbjct: 6 EQQLYIGGRYVPASSGASFETVNPATGEVLARVQRASQADVERAVASAAA--GQKVWAAM 63 Query: 79 APAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKV 138 +R L R ++LR+ +ELA LETLD GKP+ ++ +DI A + + A + + Sbjct: 64 TAMQRSRILRRAVEILRERNDELAELETLDTGKPLSETRFVDIVTGADVLEYYAGLVPAI 123 Query: 139 YDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPL 198 E P REP+GVV I WN+P+ +A WK PALA GN+++ KPSE +PL Sbjct: 124 EGEQIPLRETSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTPL 183 Query: 199 TAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGE 258 + +++A++ EAG+P GV NVL G G VG+ L H ++ + FTG T K++M A Sbjct: 184 SVLKLAEIYSEAGLPDGVFNVLTGSGREVGQWLTEHPGIEKISFTGGTSTGKKVMASASS 243 Query: 259 SNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318 S++K + +E GGKSP IVF DA DL AA+ A A ++ G+VCT G+R+ V R ++ +F Sbjct: 244 SSLKEVTMELGGKSPLIVFEDA-DLDRAADIAVMANFYSSGQVCTNGTRVFVPRMLQARF 302 Query: 319 LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTL--E 376 V+E +K + G+P D T G LV M +VL YI+ G ++GA+LL GG R E Sbjct: 303 EAKVLERVKRIRLGDPQDANTNFGPLVSFAHMESVLGYIDKGRQEGARLLIGGARVTDGE 362 Query: 377 ETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTS 436 G YV PT+F ++ M I +EEIFGPV+S++ +D+ +E + AND+ YGLAAG+ T Sbjct: 363 YAKGAYVAPTVFTDCSDEMCIVREEIFGPVMSILVYDSEDEVIRRANDSDYGLAAGVVTR 422 Query: 437 DISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIK 496 D+++AH+ + AG W+N + P GG+KQSG GR+ L L YT +K+ ++ Sbjct: 423 DLARAHRVIHKLEAGICWINTWGESPAEMPVGGYKQSGVGRENGLTTLAHYTRIKSVQVE 482 Query: 497 L 497 L Sbjct: 483 L 483 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: 620 Number of extensions: 30 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: 497 Length of database: 490 Length adjustment: 34 Effective length of query: 463 Effective length of database: 456 Effective search space: 211128 Effective search space used: 211128 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