Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_104913734.1 C3B54_RS06275 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_002950575.1:WP_104913734.1 Length = 488 Score = 218 bits (555), Expect = 4e-61 Identities = 145/456 (31%), Positives = 230/456 (50%), Gaps = 19/456 (4%) Query: 42 PVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEEL 101 P G + +A C A+ N AV A F +G L A+R L A L +E Sbjct: 33 PFTGESVGTIADCGSAEVNSAVAAALRAFKTG----LPRAQRITILEEAARGLDTRRDEF 88 Query: 102 ALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVAPTPHDQLG-----LVTRE 156 A + L+ GK + D + ++ A + + +TA V P + G + R Sbjct: 89 AAVIALETGKSLKDCRT-EVARATETLRYTAAEARTQSSRVIPADAAEAGEGALAMEMRV 147 Query: 157 PVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGV 216 P GVVGAI P+NFPL + K+ PALA G SVV KP+ ++PLTA+ + L EAG+ AG Sbjct: 148 PRGVVGAITPFNFPLNTSVHKVAPALAVGCSVVHKPAHQTPLTALALQDLFREAGLGAGW 207 Query: 217 LNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIV 276 L V G G+AL H DV + FTGS + ++ A ++ K++ LE G +P ++ Sbjct: 208 LEVCTDGGGNAGRALVEHSDVAVISFTGSNVVGWEI---AQKAPKKKVLLELGSNAP-VI 263 Query: 277 FADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLD 336 + DL AA+ A+ + G+ C + R++ +SI K + + G+P D Sbjct: 264 VTETADLAHAAKRIATGGFGSAGQSCISVQRVIAHQSIASKLEDHLAAVAGEIQAGDPFD 323 Query: 337 PQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMR 396 P+ +G L+ + + V +++ + G ++ + P I G R Sbjct: 324 PKVDIGPLISLEASSRVREWVQEAVEMGGAIVG----NTPNNDSVAIAPIIISGAPEKSR 379 Query: 397 IAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVN 456 I Q+EIFGPV++V+ ++T +EA+AIANDT +GL AG++TSD+S+ + G V +N Sbjct: 380 IRQKEIFGPVITVLPYNTFDEALAIANDTIFGLQAGVFTSDVSEMLSAFHQLEFGGVLIN 439 Query: 457 QYDGGDMT-APFGGFKQSGNGRDKSLHALEKYTELK 491 + P+GG +SGN R+ +A+E+ T L+ Sbjct: 440 DIPTVRLDHQPYGGVAESGNTREGPHYAMEELTHLR 475 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: 581 Number of extensions: 32 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: 488 Length adjustment: 34 Effective length of query: 463 Effective length of database: 454 Effective search space: 210202 Effective search space used: 210202 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