Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Pedo557:CA265_RS14635 Length = 501 Score = 355 bits (912), Expect = e-102 Identities = 200/477 (41%), Positives = 279/477 (58%), Gaps = 14/477 (2%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 +I G++ V G F+ +SP+DG+ K A D AV+ A F + WS+ + + Sbjct: 17 YIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAFKT--WSKTSSTE 74 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R L + A + N+E LA +ET+D GK + ++ + D+P + A I + Sbjct: 75 RSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEGSL 134 Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 + + + L+ EP+GVV I+PWNFPLLM WKL PALA GN VVLKP+E +P++ + Sbjct: 135 SELDQNTVSLIVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVSIMV 194 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 + +L + +P GV+NV+ G+G +G+AL + V FTGST + +M YA E N+ Sbjct: 195 LMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYATE-NII 252 Query: 263 RIWLEAGGKSPNIVFA-----DAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDK 317 + LE GGKSPNI F+ D L A E A A NQGE+CT SRLL++ I +K Sbjct: 253 PVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVM-FALNQGEICTCPSRLLIQEDIYEK 311 Query: 318 FLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTL-- 375 F+ V+E K K G+PLD +GA Q + +YI+ G ++GA++L GG+ Sbjct: 312 FIAKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEINELP 371 Query: 376 -EETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIW 434 E GG Y++PTIF G N MRI QEEIFGPVL+V F T EEA+ IANDT YGL AG+W Sbjct: 372 GELGGGYYIKPTIFKG-HNKMRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGAGVW 430 Query: 435 TSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELK 491 T D + ++ RA++AG VWVNQY APFGG+KQSG GR+ L Y + K Sbjct: 431 TRDAHELYQVPRAIQAGRVWVNQYHAYPAGAPFGGYKQSGVGRENHKMMLGHYRQTK 487 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: 638 Number of extensions: 29 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: 501 Length adjustment: 34 Effective length of query: 463 Effective length of database: 467 Effective search space: 216221 Effective search space used: 216221 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