Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate CA265_RS24850 CA265_RS24850 aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Pedo557:CA265_RS24850 Length = 454 Score = 221 bits (562), Expect = 5e-62 Identities = 147/418 (35%), Positives = 213/418 (50%), Gaps = 7/418 (1%) Query: 75 WSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEA 134 W+ +R A + F+DLL +E+LA + T ++GKP+ S + +I GA I W Sbjct: 37 WAGKTLQERIAVITHFSDLLEVEIEKLASVLTSEVGKPLQQSRN-EINGARARIKWMLAN 95 Query: 135 IDK-VYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPS 193 +K + DEV ++ EP+GVV I WN+P L+ PAL +GN+V+ KPS Sbjct: 96 AEKYLADEVMTDEPGIKEIIKYEPLGVVCNISAWNYPYLVGVNVFIPALLSGNTVMYKPS 155 Query: 194 EKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLM 253 E + LT I I +L +AG+P V ++ G T G AL L+MD + FTGS K K L+ Sbjct: 156 EYATLTGIEIEKLLKKAGVPDDVFHIAIGAKET-GSAL-LNMDFNGYFFTGSYKTGK-LI 212 Query: 254 VYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERS 313 + M LE GGK P + D D+ AAA A +N G+ C A R+ V+ Sbjct: 213 YEKVAAKMVPCQLELGGKDPLYITDDVTDVAAAAIGTADGAFYNNGQSCCAVERIYVQEK 272 Query: 314 IKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKR 373 D + V +K WK G P +GAL +Q++ + + ++ GAKLL GGK Sbjct: 273 NYDDYCNAFVTEVKSWKTGIPTAEGVYIGALTRKEQISVLENQVKDALNKGAKLLTGGKA 332 Query: 374 TLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGI 433 E G Y EPT+ VTN M + QEE FGP++ ++ EA+ + DT YGL A + Sbjct: 333 V--EGKGYYFEPTVLTDVTNDMLVMQEESFGPIIGIMKVKDDAEALKMMKDTDYGLTASV 390 Query: 434 WTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 +T+ +A K + AGS + N D P+ G K SG G S + +T+ K Sbjct: 391 YTASQERAEKILAQLDAGSGYWNCCDRVSAALPWSGRKYSGIGATLSHQGIRAFTKPK 448 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: 490 Number of extensions: 15 Number of successful extensions: 3 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: 454 Length adjustment: 33 Effective length of query: 464 Effective length of database: 421 Effective search space: 195344 Effective search space used: 195344 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: 51 (24.3 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