Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate BPHYT_RS20795 BPHYT_RS20795 sorbosone dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__BFirm:BPHYT_RS20795 Length = 502 Score = 369 bits (947), Expect = e-106 Identities = 208/476 (43%), Positives = 292/476 (61%), Gaps = 5/476 (1%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 FI+G+ +GE SP G + + D N AV +AR F+ G WS+L+ + Sbjct: 23 FIDGKDYAGNTGEFVTRKSPGHGVPVTATPRACVDDLNAAVASARRAFDDGRWSRLSGEQ 82 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R L++ A L+R VE LA LETL+ GKPIG S +I AA + A V+ + Sbjct: 83 RATVLLKTARLIRDKVETLAYLETLESGKPIGQSRG-EINAAAGIWEYAAGLARVVHGDS 141 Query: 143 APT-PHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAI 201 T D GL R+P+GVVG + PWNFP + +L LA G + V+KP+E + T + Sbjct: 142 HDTLGADLFGLTVRQPIGVVGIVTPWNFPFFILSERLPFVLAAGCTAVVKPAELTSTTTL 201 Query: 202 RIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNM 261 ++A L EAG+P GV+NV+ G G VG+ALA HMDVD + FTGST + + ++ AG NM Sbjct: 202 KLAALLTEAGLPDGVVNVVTGLGAVVGQALAEHMDVDMMSFTGSTPVGRSVLAAAG-GNM 260 Query: 262 KRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPM 321 K++ LE GGK+P IVFADA DL AA+A A I FN G+ C +GSRL+V RS++++ + Sbjct: 261 KKVGLELGGKNPQIVFADA-DLDDAADAIAFGICFNAGQCCVSGSRLVVHRSVEEELVAR 319 Query: 322 VVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGT 381 V + + G+PLD VGA+V+ +Q + + +I+AG +DGA+L+ GG+ T Sbjct: 320 VKAVFEKVRVGDPLDASNHVGAIVEARQFDKIRGFIDAGRRDGAQLVHGGEST-SHGERF 378 Query: 382 YVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKA 441 +++PT+F V +AQEEIFGPVLSV +FDT EEA+ +AN PYGLAA IWT D+ A Sbjct: 379 FIQPTLFRNVQPQSALAQEEIFGPVLSVTSFDTFEEAIQLANGVPYGLAASIWTRDLQGA 438 Query: 442 HKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497 + R V+AG +WVN G P GG KQSG GR+ + +E+YTELK+ ++L Sbjct: 439 ISSFREVQAGRIWVNCTITGGPEMPIGGVKQSGIGRETGRYGVEEYTELKSVHVQL 494 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: 666 Number of extensions: 33 Number of successful extensions: 5 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 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