Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate AO353_29295 AO353_29295 aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__pseudo3_N2E3:AO353_29295 Length = 496 Score = 777 bits (2006), Expect = 0.0 Identities = 380/494 (76%), Positives = 433/494 (87%) Query: 4 LTRADWEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAV 63 +TR+ WEQ Q L IEGRAFI+G Y A+S +TFEC+SPVDGRFLA VAS D ADAN AV Sbjct: 3 ITRSGWEQHFQSLTIEGRAFIDGHYCSALSRDTFECVSPVDGRFLANVASTDEADANAAV 62 Query: 64 ENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPG 123 + AR F+SGVW++LAPA+RK LIRFADL+ N EELALLETLDMGKPI DS +IDIP Sbjct: 63 QVARRAFDSGVWAKLAPAERKRILIRFADLILANQEELALLETLDMGKPISDSMAIDIPA 122 Query: 124 AAQAIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALA 183 A AI W+AEAIDK+YDEVA TPHDQLGLVTREP GVV AIVPWNFPL+MA WK PALA Sbjct: 123 TANAIRWSAEAIDKIYDEVAATPHDQLGLVTREPSGVVAAIVPWNFPLIMASWKFAPALA 182 Query: 184 TGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFT 243 GNS +LKPSEKSPLTAIRIAQLA++AGIP GV NVLPG+GHTVGKALALHMDVD L FT Sbjct: 183 AGNSFILKPSEKSPLTAIRIAQLALDAGIPKGVFNVLPGFGHTVGKALALHMDVDVLAFT 242 Query: 244 GSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCT 303 GST IAKQL++YAG+SNMKR+WLEAGGKSPN+VFADAPDL+AAA AAASAIAFNQGEVCT Sbjct: 243 GSTAIAKQLLIYAGQSNMKRVWLEAGGKSPNVVFADAPDLRAAATAAASAIAFNQGEVCT 302 Query: 304 AGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKD 363 AGSRLLVERSI+++F+P++VEAL+ WKPG+ LDP+TTVGA+VD +Q++ VL YI G + Sbjct: 303 AGSRLLVERSIREQFIPLLVEALQAWKPGHALDPETTVGAVVDQRQLDNVLRYISIGKEQ 362 Query: 364 GAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIAN 423 GA+L+AGG R LE+TGG YVEP IFDGVTNAM IA+EEIFGPVLS+I FDTAEEA+AIAN Sbjct: 363 GAQLIAGGNRALEDTGGLYVEPAIFDGVTNAMTIAREEIFGPVLSLITFDTAEEALAIAN 422 Query: 424 DTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHA 483 D+ +GLAAG+WTS++SKAH AR +RAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHA Sbjct: 423 DSIFGLAAGVWTSNLSKAHTFARGLRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHA 482 Query: 484 LEKYTELKATWIKL 497 +KYTELKATWIKL Sbjct: 483 FDKYTELKATWIKL 496 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: 757 Number of extensions: 18 Number of successful extensions: 2 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: 496 Length adjustment: 34 Effective length of query: 463 Effective length of database: 462 Effective search space: 213906 Effective search space used: 213906 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