Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_009562902.1 RSPH17029_RS04350 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_000015985.1:WP_009562902.1 Length = 483 Score = 339 bits (870), Expect = 1e-97 Identities = 186/474 (39%), Positives = 289/474 (60%), Gaps = 10/474 (2%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVEN-ARATFNSGVWSQLAPA 81 F++G + +G + P G +A++ A A+ + ARA W+ + P Sbjct: 10 FVDGRPLEDETGAPIPVIYPATGEEIARLHEATPAVIEAALASGARA---QAAWAAMRPV 66 Query: 82 KRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDE 141 +R L R +DL+R EEL+LLETLD GKP+ ++ D A A+ + A V E Sbjct: 67 ERARILRRASDLIRARNEELSLLETLDTGKPLQETLVADWASGADALEFFAGLAPAVTGE 126 Query: 142 VAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAI 201 P D + + REP+G+ I WN+P +ACWK PALA GN++V KPSE +PL A+ Sbjct: 127 TVPLGQDFVYTI-REPLGLCVGIGAWNYPSQIACWKAAPALALGNAMVFKPSEVTPLGAL 185 Query: 202 RIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNM 261 ++A++ IEAG+P G+ NV+ G G VG AL V + TGS +++ A E + Sbjct: 186 KLAEILIEAGLPPGLFNVVQGRG-AVGAALVTDSRVAKVSLTGSVPTGRRVYAAAAEG-V 243 Query: 262 KRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPM 321 + + +E GGKSP IVF DA DL++A AA ++ G++C+ G+R+ V++ IK+ FL Sbjct: 244 RHVTMELGGKSPLIVFDDA-DLESAIGAAMLGNFYSAGQICSNGTRVFVQKGIKEAFLAR 302 Query: 322 VVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGT 381 + E + G+PLDP+ +G LV Q+ VL+YIE +G +L+ GG+ ++ G Sbjct: 303 LAERADAIRMGDPLDPEVQMGPLVSQAQLEKVLAYIEKARAEGGRLVCGGEASVSP--GC 360 Query: 382 YVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKA 441 YV+PT+F VT+AM +A+EE+FGPV++V+ F+T EEA+A AN T +GLAAG++T+D+++A Sbjct: 361 YVQPTVFADVTDAMTLAREEVFGPVMAVLDFETEEEAIARANATDFGLAAGVFTADLTRA 420 Query: 442 HKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWI 495 H+ ++AG+ W+N Y+ + APFGG K SG GR+ A+E YT++K+ ++ Sbjct: 421 HRVVAQLQAGTCWINAYNLTPVEAPFGGVKLSGVGRENGRAAVEHYTQVKSVYV 474 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: 632 Number of extensions: 27 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: 483 Length adjustment: 34 Effective length of query: 463 Effective length of database: 449 Effective search space: 207887 Effective search space used: 207887 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 Apr 10 2024. 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