Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate AZOBR_RS09720 AZOBR_RS09720 succinate-semialdehyde dehdyrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__azobra:AZOBR_RS09720 Length = 497 Score = 315 bits (808), Expect = 2e-90 Identities = 191/483 (39%), Positives = 280/483 (57%), Gaps = 15/483 (3%) Query: 13 AQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNS 72 A+ L+ +G F++G + DA SG+T E +P DG L V + RA+E A + + Sbjct: 17 AELLRFQG--FVDGRWIDADSGKTVEVTNPADGSVLGSVPMMGADETRRAIEAAERAWPA 74 Query: 73 GVWSQLAPAKRKAKLIR-FADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWT 131 W L AK +AK +R + DL+ N E++A + T + GKP+ ++ ++ AA I W Sbjct: 75 --WRALT-AKERAKTLRTWFDLMMANQEDIARIMTAEQGKPLAEARG-EVAYAASFIEWF 130 Query: 132 AEAIDKVYDEVAPT--PHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVV 189 AE +VY + P P ++ +VT+EP+GV AI PWNFP M K GPALA G +V Sbjct: 131 AEEGKRVYGDTIPQHLPGRRI-VVTKEPIGVTAAITPWNFPAAMITRKAGPALAAGCPMV 189 Query: 190 LKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIA 249 +KP+ +PLTA+ +A LA AGIPAG+L+V+ G +G + + V L FTGST+I Sbjct: 190 IKPATATPLTALAMAVLAERAGIPAGILSVVTGSARAIGGEMTGNPTVRKLTFTGSTEIG 249 Query: 250 KQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLL 309 K+LM +K++ LE GG +P +VF DA DL A + A ++ N G+ C +RLL Sbjct: 250 KELMAQCA-GTVKKVSLELGGNAPFLVFNDA-DLDEAVKGAIASKYRNTGQTCVCANRLL 307 Query: 310 VERSIKDKFLPMVVEALKGWKPGNPLDPQ-TTVGALVDTQQMNTVLSYIEAGHKDGAKLL 368 V+ + D F + EA+K K G L + G L+D + V +I + GA+++ Sbjct: 308 VQSGVYDAFAAKLAEAVKALKVGPGLTTEGAQQGPLIDMAAVEKVEDHIRDATEKGARVV 367 Query: 369 AGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYG 428 GGKR E GG++ EPTI VT AM++A+EE FGPV + F+T EEAV +AN T +G Sbjct: 368 LGGKR--HELGGSFFEPTILADVTPAMKVAREETFGPVAPLFRFETEEEAVRMANATEFG 425 Query: 429 LAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYT 488 LAA ++ DI + + A A+ G V +N+ APFGG K+SG GR+ S + +E Y Sbjct: 426 LAAYFYSRDIGRVWRVAEALEYGIVGINEGIISTEVAPFGGMKESGIGREGSKYGIEDYL 485 Query: 489 ELK 491 E+K Sbjct: 486 EIK 488 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: 632 Number of extensions: 34 Number of successful extensions: 8 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: 497 Length adjustment: 34 Effective length of query: 463 Effective length of database: 463 Effective search space: 214369 Effective search space used: 214369 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