Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__PV4:5210745 Length = 485 Score = 295 bits (755), Expect = 2e-84 Identities = 176/472 (37%), Positives = 267/472 (56%), Gaps = 11/472 (2%) Query: 22 AFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPA 81 ++I+G +T V + F+ ++P +A+V L D A+ A+ WS+ + Sbjct: 14 SYIDGRWT--VGEQRFDVVNPASQEVIAQVVDASLDDTQEAILAAKRALPE--WSKRSAN 69 Query: 82 KRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDE 141 +R A + ++ +L+ ++ E+L L TL+ GKP+ ++ +I A I W AE +VY + Sbjct: 70 ERAALMRKWFNLMMEHQEDLGRLLTLEQGKPLAEAKG-EIAYGAAFIDWFAEEGKRVYGD 128 Query: 142 VAPTP-HDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTA 200 P P +D+ LV ++PVGVV +I PWNFP M K ALA G + V +PS +PL+A Sbjct: 129 TIPAPANDKRILVIKQPVGVVASITPWNFPNAMIARKAAAALAAGCTFVARPSPLTPLSA 188 Query: 201 IRIAQLAIEAGIPAGVLNVLPGYGHT-VGKALALHMDVDTLVFTGSTKIAKQLMVYAGES 259 + +A+LA AGIPAGV N++ G +GK L H DV FTGST + K L+ S Sbjct: 189 LAMAELAERAGIPAGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKILLAQCATS 248 Query: 260 NMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFL 319 +K++ +E GG +P IVF DA D+ AA + A + N G+ C +R+ V++ + F Sbjct: 249 -VKKVSMELGGNAPFIVFDDA-DIDAAVQGALISKYRNAGQTCVCTNRIFVQKGVAAAFT 306 Query: 320 PMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETG 379 A+ K G+ L TVG ++ + VL ++ GAKL+ GG+ + E G Sbjct: 307 EKFTAAVANLKLGDGLGDGVTVGPMISKDAVQNVLKLVDDTVASGAKLVTGGQPS--ELG 364 Query: 380 GTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDIS 439 +++ P I VTN M +A+ EIFGPV +I+FD+ EA+A+ANDT YGLAA + DI Sbjct: 365 ESFLAPVIVTDVTNEMPLARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYARDIG 424 Query: 440 KAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 + + A + G V VN+ + APFGG KQSGNGR+ S + L+ Y E+K Sbjct: 425 RIFRVAEGLEYGMVGVNEGIISNAAAPFGGVKQSGNGREGSKYGLDDYLEIK 476 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: 541 Number of extensions: 19 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: 485 Length adjustment: 34 Effective length of query: 463 Effective length of database: 451 Effective search space: 208813 Effective search space used: 208813 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