Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate Ga0059261_1680 Ga0059261_1680 NAD-dependent aldehyde dehydrogenases
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Korea:Ga0059261_1680 Length = 469 Score = 253 bits (646), Expect = 1e-71 Identities = 163/460 (35%), Positives = 244/460 (53%), Gaps = 17/460 (3%) Query: 35 ETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKRKAKLIRFADLL 94 ETF + P GR A AD + AV AR F W+ R A ++ AD + Sbjct: 17 ETFPVIDPATGRPFADAPLASTADLDAAVAAARRAFPG--WAATPIEDRAAAILAIADSI 74 Query: 95 RKNVEELALLETLDMGKPIGDSSSIDIPGA---AQAIHWTAEAIDKVYDEVAPTPHDQLG 151 +ELA L + + GKP+ ++ +I GA A+A A+D + D+ + Sbjct: 75 EAAKDELARLLSAEQGKPVPNAVG-EIMGALAWARATAGLRPAVDVLKDDDSVRVE---- 129 Query: 152 LVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRIAQLAIEAG 211 V R+P+GVV +I PWNFP+++A W + P L GN+VV+KPS +PL A+R+ ++A A Sbjct: 130 -VHRKPLGVVASISPWNFPVMIAIWHIIPGLVAGNTVVMKPSSFTPLAALRMVEIA-NAH 187 Query: 212 IPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMKRIWLEAGGK 271 +P GVLN + G +G+A+A H +D +VFTGST + +M G +N+KR+ LE GG Sbjct: 188 LPPGVLNSVTGEVE-IGRAIASHPGIDKIVFTGSTPTGRSIMA-DGAANLKRLTLELGGN 245 Query: 272 SPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVVEALKGWKP 331 IV DA + AA+ A A N G++C A R+ V SI D + E + Sbjct: 246 DAAIVLPDADVDKVAAKIFAKAFG-NSGQICAAVKRVYVHESIHDALAEKLAEMARTAVV 304 Query: 332 GNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTYVEPTIFDGV 391 G D + G + + +Q + V + + G + LAGG+ E G + ++ V Sbjct: 305 GPGSDAASQFGPVQNRKQFDLVRALADDARAHGGRFLAGGEA--REGDGYFFPLSVVVDV 362 Query: 392 TNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAHKTARAVRAG 451 T+ MRI EE FGP+L VI + E+A+A AN GL +W++D + A A+ + AG Sbjct: 363 TDGMRIVDEEQFGPILPVIRYSDPEDALARANANENGLGGSVWSADPAAALAFAQRLEAG 422 Query: 452 SVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 +VWVN + PFGG KQSG G + L+ LE+Y +L+ Sbjct: 423 TVWVNDHASISPDVPFGGAKQSGVGTEFGLYGLEEYMQLQ 462 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: 590 Number of extensions: 27 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: 469 Length adjustment: 34 Effective length of query: 463 Effective length of database: 435 Effective search space: 201405 Effective search space used: 201405 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