Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate PP_2487 PP_2487 putative aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Putida:PP_2487 Length = 503 Score = 390 bits (1001), Expect = e-113 Identities = 206/477 (43%), Positives = 297/477 (62%), Gaps = 7/477 (1%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 FI+ ++ A GET + ++P +G+ L + + AD +RAV+ A+ F + W +PA+ Sbjct: 24 FIDNQWVTAEYGETLDIINPANGKILTNIPNATAADVDRAVQAAQRAFVT--WRTTSPAE 81 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R L++ ADLL + + A+LETLD+GKPI +S S+DIP A + A I DE Sbjct: 82 RANALLKIADLLEADADRFAVLETLDVGKPIRESRSVDIPLAIDHFRYFAGVIRSQSDEA 141 Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 L + EP+GVVG ++PWNFPLLMA WK+ PA+A GN+VV+KPSE +P+T + Sbjct: 142 VMLDEQTLSIALSEPLGVVGQVIPWNFPLLMAAWKIAPAIAAGNTVVIKPSELTPVTILE 201 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 +A++ + +PAGV+N++ G G TVG+AL H D+ L FTGST++ +L+ A + Sbjct: 202 LAKIFAKV-LPAGVVNIVTGLGTTVGQALLDHPDLRKLAFTGSTRVG-ELVANAAAKKII 259 Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMV 322 LE GGKS NIVF DA + A E A AI +NQG+VC +G+RL V SI ++FL + Sbjct: 260 PATLELGGKSANIVFPDA-NWDKAVEGAVLAILWNQGQVCESGARLFVHESIYERFLAEL 318 Query: 323 VEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRT--LEETGG 380 + + G+PL+P T +GA V QM +L Y++ ++GA++L GG R + G Sbjct: 319 KHKFEAVRVGDPLNPDTMMGAQVSKTQMERILGYVDIAKEEGAEVLIGGGRLTGADYDAG 378 Query: 381 TYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISK 440 +++PTI GV N MR+A EEIFGPVL VI F E +A+AND+ YGLA +WT DI++ Sbjct: 379 FFIQPTILVGVRNDMRVAYEEIFGPVLCVIPFKDEAEVIAMANDSEYGLAGAVWTQDINR 438 Query: 441 AHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497 A + ARAV G +WVN Y APFGG+K+SG GR+ LE Y++ K ++ L Sbjct: 439 ALRVARAVETGRMWVNTYHEIPAHAPFGGYKKSGLGRETHKSMLEAYSQKKNIYVSL 495 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: 625 Number of extensions: 23 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: 503 Length adjustment: 34 Effective length of query: 463 Effective length of database: 469 Effective search space: 217147 Effective search space used: 217147 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