Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate RR42_RS26255 RR42_RS26255 aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Cup4G11:RR42_RS26255 Length = 499 Score = 573 bits (1477), Expect = e-168 Identities = 276/491 (56%), Positives = 361/491 (73%) Query: 7 ADWEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENA 66 A W ++A + I +A+I+G + DA G TFE ++P G+ LA+VA+C D +RAV A Sbjct: 8 AYWRKQAATVSIRSQAYIDGRWADAADGATFETINPATGKALARVAACGAQDVDRAVAAA 67 Query: 67 RATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQ 126 R F SGVWS + RKA L+R + L+ + EELALLETLDMGKPI ++ DIP A + Sbjct: 68 RKAFQSGVWSDTPRSARKATLLRLSHLIETHREELALLETLDMGKPIAETLQYDIPEAGR 127 Query: 127 AIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGN 186 W AEAIDK+YDE+APT L +TREP+GVV A+VPWN+PLLMA WK+ PALA GN Sbjct: 128 TYAWYAEAIDKIYDEIAPTGPGVLATITREPLGVVAAVVPWNYPLLMASWKVAPALAAGN 187 Query: 187 SVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGST 246 SVVLKP+E+SPLTA+R+A+LA EAGIPAGV NV+PG G G+AL H DVD + FTGST Sbjct: 188 SVVLKPAEQSPLTALRLAELAEEAGIPAGVFNVVPGLGAAAGQALGRHPDVDCIAFTGST 247 Query: 247 KIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGS 306 K+ M Y+G+SN+KR+WLE GGKSP+IVF D PDL AA+AAA I NQGE+C AGS Sbjct: 248 ATGKRFMEYSGQSNLKRVWLECGGKSPHIVFDDCPDLDRAAQAAAIGIFSNQGEICIAGS 307 Query: 307 RLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAK 366 RL V+ I D F+ + +PG+PLDP T +GA+VD Q+ V+SY+++G +GA+ Sbjct: 308 RLYVQSGIYDAFMEKLEAHAARMQPGDPLDPATAMGAIVDGAQLQRVMSYVKSGEDEGAR 367 Query: 367 LLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTP 426 L AGGKR ++GG Y++PTIF+ T ++ I +EEIFGPVL+V F++ EEA+ +AND+P Sbjct: 368 LRAGGKRAHTDSGGFYMQPTIFECPTQSLTIVREEIFGPVLAVTRFESEEEAIRMANDSP 427 Query: 427 YGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEK 486 YGL +G+WTS++S+AH+ +R ++AG VWVN Y D+T PFGG KQSG+GRDKSLHAL+K Sbjct: 428 YGLGSGLWTSNLSRAHRVSRKLQAGLVWVNCYMDSDVTVPFGGVKQSGSGRDKSLHALDK 487 Query: 487 YTELKATWIKL 497 YT+LK TWI L Sbjct: 488 YTDLKTTWISL 498 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: 698 Number of extensions: 23 Number of successful extensions: 1 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: 499 Length adjustment: 34 Effective length of query: 463 Effective length of database: 465 Effective search space: 215295 Effective search space used: 215295 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