Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 14450 b0312 betaine aldehyde dehydrogenase, NAD-dependent (NCBI)
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Keio:14450 Length = 490 Score = 357 bits (915), Expect = e-103 Identities = 189/482 (39%), Positives = 286/482 (59%), Gaps = 7/482 (1%) Query: 19 EGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQL 78 E + +I+G YT A SG TFE ++P +G LA V + D +RAV++A+ +W+ + Sbjct: 6 EQQLYIHGGYTSATSGRTFETINPANGNVLATVQAAGREDVDRAVKSAQQ--GQKIWASM 63 Query: 79 APAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKV 138 +R L R D+LR+ +ELA LETLD GK ++S++DI A + + A I + Sbjct: 64 TAMERSRILRRAVDILRERNDELAKLETLDTGKAYSETSTVDIVTGADVLEYYAGLIPAL 123 Query: 139 YDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPL 198 P REP+GVV I WN+P+ +A WK PALA GN+++ KPSE +PL Sbjct: 124 EGSQIPLRETSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTPL 183 Query: 199 TAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGE 258 TA+++A++ EAG+P GV NVLPG G G+ L H + + FTG K++M + Sbjct: 184 TALKLAEIYSEAGLPDGVFNVLPGVGAETGQYLTEHPGIAKVSFTGGVASGKKVMANSAA 243 Query: 259 SNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKF 318 S++K + +E GGKSP IVF DA DL AA+ A A F+ G+VCT G+R+ V K F Sbjct: 244 SSLKEVTMELGGKSPLIVFDDA-DLDLAADIAMMANFFSSGQVCTNGTRVFVPAKCKAAF 302 Query: 319 LPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEET 378 ++ ++ + G+ DPQT G LV + VL YI G ++GA++L GG L+ Sbjct: 303 EQKILARVERIRAGDVFDPQTNFGPLVSFPHRDNVLRYIAKGKEEGARVLCGGD-VLKGD 361 Query: 379 G---GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWT 435 G G +V PT+F ++ M I +EEIFGPV+S++ +++ +E + ANDT YGLAAGI T Sbjct: 362 GFDNGAWVAPTVFTDCSDDMTIVREEIFGPVMSILTYESEDEVIRRANDTDYGLAAGIVT 421 Query: 436 SDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWI 495 +D+++AH+ + AG W+N + P GG+K SG GR+ + L+ YT++K+ + Sbjct: 422 ADLNRAHRVIHQLEAGICWINTWGESPAEMPVGGYKHSGIGRENGVMTLQSYTQVKSIQV 481 Query: 496 KL 497 ++ Sbjct: 482 EM 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: 627 Number of extensions: 34 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 17 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