Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein
Query= metacyc::MONOMER-11560 (497 letters) >NCBI__GCF_000012965.1:WP_011373513.1 Length = 471 Score = 189 bits (481), Expect = 1e-52 Identities = 138/467 (29%), Positives = 234/467 (50%), Gaps = 28/467 (5%) Query: 40 LSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKRKAKLIRFADLLRKNVE 99 ++P +G ++ +C+ DA +A+ A S+ A+R + L+ A L +N E Sbjct: 21 VNPYNGEVASEFVTCNADDAKKALNIALLASKEA--SKTTIAQRCSWLLDVASKLAQNKE 78 Query: 100 ELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVAPTPHDQLGLVT----- 154 ++A T ++GKPI S I++ + + AE + ++ E T G T Sbjct: 79 DIAKTITDEVGKPI-TYSRIEVERCIETVTLAAETMRTMHGETVNTDAFASGKKTISFFS 137 Query: 155 REPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRIAQLAIEAGIP- 213 R P GVV AI P+NFPL + K+ PAL GN+V+LKP+ ++PLTA + A+L IE+ Sbjct: 138 RVPCGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESEFAI 197 Query: 214 AGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMKRIWLEAGGKSP 273 L+V+ G VG L + FTGS + + + AG +K++ LE GG + Sbjct: 198 KDALSVVYG-DADVGGTLVTSEIPRVISFTGSVGVGEIITKSAG---IKKVSLELGGNAA 253 Query: 274 NIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVVEALKGWKPGN 333 + A +L AA+ A N G+VC + R+ V + I +F + EA K G+ Sbjct: 254 TFIDKSA-NLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLVVGS 312 Query: 334 PLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTYVEPTIFDGVTN 393 P + T +G LV+ + + ++++ K+GA + + G P + V Sbjct: 313 PYEEDTFMGPLVNDEAAKRAMEWVQSAIKEGATPILEPR-----VEGRVFYPCVMADVKE 367 Query: 394 AMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAHKTARAVRAGSV 453 M I +E+F P++S+I +EA+ + N++PYGL I+T+D++ + + AG + Sbjct: 368 DMAIVCQEVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINELDAGGI 427 Query: 454 WVN-----QYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWI 495 +N ++D P+GG K SG GR+ A+E+ +E+K+ I Sbjct: 428 VINDMPTLRFD----IQPYGGVKLSGVGREGPRFAIEEMSEIKSVII 470 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: 495 Number of extensions: 31 Number of successful extensions: 4 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: 471 Length adjustment: 34 Effective length of query: 463 Effective length of database: 437 Effective search space: 202331 Effective search space used: 202331 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 09 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