Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_086509869.1 BZY95_RS10455 aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_002151265.1:WP_086509869.1 Length = 502 Score = 585 bits (1508), Expect = e-171 Identities = 293/496 (59%), Positives = 363/496 (73%), Gaps = 3/496 (0%) Query: 2 TTLTRADWEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANR 61 T T ADW+ RA +L E RAFI+ + A SG TFE +P G LA+VASCD DA R Sbjct: 7 TPRTLADWQARAAELSFESRAFIDDSFVAAESGATFESRNPATGEILAQVASCDEPDAAR 66 Query: 62 AVENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDI 121 AV AR F G WS+LAP KRK L+ ADL+ + ELAL++TLDMGKPI S D+ Sbjct: 67 AVAVARRAFADGAWSRLAPGKRKKTLLHLADLMEAHKHELALIDTLDMGKPIASSLG-DM 125 Query: 122 PGAAQAIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPA 181 GA I + AE IDK+Y EVAPT + L LV REP+GVV AIVPWNFPL+M WK+ PA Sbjct: 126 AGAIACIRYQAECIDKLYGEVAPTGEETLALVLREPIGVVAAIVPWNFPLMMTAWKIAPA 185 Query: 182 LATGNSVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLV 241 LA GNSV+LKPSEKSPL+A+R+AQLA EAGIP GV VLPG+GHTVGKALAL M+VD L Sbjct: 186 LAAGNSVILKPSEKSPLSALRLAQLAQEAGIPRGVFQVLPGFGHTVGKALALSMEVDCLA 245 Query: 242 FTGSTKIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEV 301 FTGST + KQLM YAG+SN+KR++LE GGKSPN+VFAD DL A AA+AI NQGEV Sbjct: 246 FTGSTAVGKQLMQYAGQSNLKRVYLECGGKSPNLVFADCKDLDTVASHAAAAIFHNQGEV 305 Query: 302 CTAGSRLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGH 361 C AGSRLLVE +I+D F+ V++A + +PG+PLDP + +GA+VD Q +L YI G Sbjct: 306 CIAGSRLLVENTIRDDFVERVLKAAENMQPGDPLDPDSFMGAIVDEAQHRRILDYIRQGV 365 Query: 362 KDGAKLLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAI 421 ++GA+L GG+ + G ++ PT+FDGVT M I +EEIFGPVL+V+ FDT EEAVA+ Sbjct: 366 EEGARLRTGGQAI--DGPGLFIPPTVFDGVTPQMTIGREEIFGPVLAVLGFDTEEEAVAM 423 Query: 422 ANDTPYGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSL 481 ANDTPYGLAAG+W+ DI + + R +++G V+VN + GGD T PFGG KQSGNGRDKS Sbjct: 424 ANDTPYGLAAGLWSQDIDRIMRVTRRLQSGQVFVNNWAGGDQTMPFGGVKQSGNGRDKSH 483 Query: 482 HALEKYTELKATWIKL 497 H+LE+Y+ELK+ W+ L Sbjct: 484 HSLEEYSELKSVWMSL 499 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: 687 Number of extensions: 28 Number of successful extensions: 3 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: 502 Length adjustment: 34 Effective length of query: 463 Effective length of database: 468 Effective search space: 216684 Effective search space used: 216684 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 24 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