Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF3171 PGA1_c32220 5-carboxymethyl-2-hydroxymuconic semialdehyde dehydrogenase HpcC
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Phaeo:GFF3171 Length = 503 Score = 327 bits (838), Expect = 6e-94 Identities = 187/455 (41%), Positives = 259/455 (56%), Gaps = 7/455 (1%) Query: 37 FECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKRKAKLIRFADLLRK 96 F+ +SPVD + VA AD + A + AR F W L +RK LIR A+ + Sbjct: 39 FQTISPVDKSVICDVAHGTAADIDAAAQAARQAFAE--WRDLPAVQRKKILIRIAEGIEA 96 Query: 97 NVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVAPTPHDQLGLVTRE 156 EE+AL E D G+ S + GA ++ + + + +P + + TR Sbjct: 97 RAEEIALCECWDTGQAYKFMSKAALRGAENFRYFADQVVQARDGQHLQSP-TLMNVTTRV 155 Query: 157 PVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGV 216 P+G VG I PWN P +++ WK+ PALA G +VV KP+E SPLTA + ++A EAG+P GV Sbjct: 156 PIGPVGVITPWNTPFMLSTWKIAPALAAGCTVVHKPAEASPLTARLLVEIAEEAGLPPGV 215 Query: 217 LNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIV 276 LN + G+G GKAL H + + F G ++ L+ G +KR LE GGK+P IV Sbjct: 216 LNTVNGFGDEAGKALCEHPAIRAIAFVGESRTGS-LITKQGADTLKRNHLELGGKNPVIV 274 Query: 277 FADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLD 336 F DA DL+ A +A I GE CT+ SRLL++ SI+D F ++E + K G+PLD Sbjct: 275 FEDA-DLERALDAVIFMIYSINGERCTSSSRLLIQDSIRDDFEARLIERINNIKVGHPLD 333 Query: 337 PQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMR 396 P T +G LV + N V SY + K+GA + AGG+ EE G ++ PT+F N MR Sbjct: 334 PTTEIGPLVSEEHFNKVTSYFDIATKEGATIAAGGEPVGEE--GYFIRPTLFTDARNDMR 391 Query: 397 IAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVN 456 IAQEEIFGPVL+ I F T EA+A+ANDT YGL +WT+D+++A + + AG +WVN Sbjct: 392 IAQEEIFGPVLTSIPFTTEAEALALANDTAYGLTGYLWTNDLTRALRFTDRLEAGMIWVN 451 Query: 457 QYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 + + PFGG K SG GRD + E Y E K Sbjct: 452 SENVRHLPTPFGGVKASGIGRDGGDWSFEFYMEQK 486 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: 636 Number of extensions: 26 Number of successful extensions: 5 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