Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Pf1N1B4_171 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_171 Length = 477 Score = 386 bits (992), Expect = e-112 Identities = 217/481 (45%), Positives = 292/481 (60%), Gaps = 13/481 (2%) Query: 24 INGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKR 83 I G++ +A G+T +P G L V D +RAV AR F+ W++ P +R Sbjct: 3 IGGDWVEAGDGQTMPLHNPATGEVLCVVPRATPEDVDRAVLAARQAFDDSAWTRTRPRER 62 Query: 84 KAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVA 143 + L + ADL++++ E LA LE L+ GK + +D+ + + + A K+ Sbjct: 63 QNLLWKLADLMQRDAELLAQLECLNNGKSAAVAQVMDVQLSIDFLRYMAGWATKIEGSSV 122 Query: 144 PT-----PHDQL-GLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSP 197 P+DQ + RE VGVVGAIV WNFPLL+ACWKLGPALATG +VVLKP++++P Sbjct: 123 EVSMPLMPNDQFHSFIRREAVGVVGAIVAWNFPLLLACWKLGPALATGCTVVLKPADETP 182 Query: 198 LTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAG 257 LTA+++A+L +EAG PAGV NV+ G G T G AL + VD L FTGST + KQ+ A Sbjct: 183 LTALKLAELVLEAGYPAGVFNVVTGTGITAGSALTHNPLVDKLTFTGSTAVGKQIGKIAM 242 Query: 258 ESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317 ES M R+ LE GGKSP IV ADA DL+ AA AASAI FNQG+VC AGSRL V+R D Sbjct: 243 ES-MTRVTLELGGKSPTIVMADA-DLKTAAAGAASAIFFNQGQVCCAGSRLYVQRKHFDN 300 Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEE 377 + + + K GN LDP +G L+ +Q V YIE G + GA + GG E+ Sbjct: 301 VVADIADIANAMKLGNGLDPSVEMGPLISARQQERVYGYIEKGRESGATIACGG----EQ 356 Query: 378 TG-GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTS 436 G G +V+PT+ V + QEEIFGPVL I FD +A+ +AND+PYGL A IW++ Sbjct: 357 FGPGYFVKPTVIVDVDQQHSLVQEEIFGPVLVAIPFDDEADALRMANDSPYGLGASIWSN 416 Query: 437 DISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIK 496 D++ H+ +++GSVWVN + D PFGG+K SG GR+ A+E YTELK+ IK Sbjct: 417 DLAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGYAAIEHYTELKSVLIK 476 Query: 497 L 497 L Sbjct: 477 L 477 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: 630 Number of extensions: 28 Number of successful extensions: 6 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: 477 Length adjustment: 34 Effective length of query: 463 Effective length of database: 443 Effective search space: 205109 Effective search space used: 205109 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