Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate AZOBR_RS19635 AZOBR_RS19635 succinate-semialdehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__azobra:AZOBR_RS19635 Length = 485 Score = 316 bits (810), Expect = 1e-90 Identities = 186/479 (38%), Positives = 280/479 (58%), Gaps = 9/479 (1%) Query: 15 QLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGV 74 Q + +A++NG + DA SG+TF +P G LA+VA + +A+ A A + Sbjct: 6 QSLLRTQAYVNGVWRDAFSGKTFAVTNPATGEELAQVADVGAEETRQAINAADAALPA-- 63 Query: 75 WSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEA 134 W +R A L R+ +L+ E+LA+L TL+ GKP+ ++ ++ A I W AE Sbjct: 64 WRAKTAKERAAILRRWFELIMAAQEDLAVLMTLEQGKPLAEARG-EVAYGASFIEWFAEE 122 Query: 135 IDKVYDEVAPT-PHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPS 193 +VY +V P+ ++ +V +EP+GVV AI PWNFP M K+GPALA G ++V+KP+ Sbjct: 123 GKRVYGDVIPSFAGNKRIVVLKEPIGVVAAITPWNFPNAMITRKVGPALAAGCTIVVKPA 182 Query: 194 EKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHT-VGKALALHMDVDTLVFTGSTKIAKQL 252 E +PL+A+ +A+LA AG+PAGV N++ G +G L V L FTGST++ K L Sbjct: 183 EDTPLSALALAELAERAGVPAGVFNIVTGSDPVAIGGELTASPIVRKLSFTGSTEVGKIL 242 Query: 253 MVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVER 312 M + ++ +K++ LE GG +P IVF DA DL A + A ++ N G+ C +RLLV+ Sbjct: 243 MRQSADT-VKKVSLELGGNAPFIVFDDA-DLDEAVKGALASKYRNSGQTCVCANRLLVQA 300 Query: 313 SIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGK 372 + D F + EA+K + GN ++ T G +++ Q + V + GAK+ GGK Sbjct: 301 GVYDAFAAKLAEAVKQIRVGNGMEAGVTQGPMINGQAVEKVEELMGDALAKGAKVALGGK 360 Query: 373 RTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAG 432 R GGT+ EPTI GVT MR+A+EEIFGPV + F+T +A+ +ANDT +GLAA Sbjct: 361 R--HGLGGTFFEPTILTGVTTEMRVAREEIFGPVAPLFKFETEADAIRMANDTEFGLAAY 418 Query: 433 IWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 ++ DI + + A + G V +N+ APFGG KQSG GR+ S + +E + E+K Sbjct: 419 FYSRDIGRVWRVAEQLEYGMVGINEGILSTEVAPFGGIKQSGIGREGSKYGVEDFLEIK 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: 613 Number of extensions: 34 Number of successful extensions: 7 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