Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF2135 PGA1_c21670 betaine aldehyde dehydrogenase BetB
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Phaeo:GFF2135 Length = 485 Score = 348 bits (892), Expect = e-100 Identities = 190/475 (40%), Positives = 287/475 (60%), Gaps = 8/475 (1%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 FINGEY + +G + G +A V + A +A+ A+A + W+++ + Sbjct: 12 FINGEYVEDTAGTPIPVIYAATGEQIATVHAATPAIVEQALSTAKAAQKA--WARMTGTE 69 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R L R AD++R+ +L++LET D GKP+ ++ D A A+ + + E Sbjct: 70 RGRILRRAADIMRERNHDLSVLETYDTGKPLQETLVADATSGADALEYFGGLAASLTGEH 129 Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 P D + RE +G+ I WN+P +ACWK PALA GNS+V KPSE +PL A++ Sbjct: 130 IPLGEDWV-YTKREALGLCVGIGAWNYPTQIACWKGAPALACGNSMVFKPSETTPLCALK 188 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 +A++ IEAG PAGV NV+ G G VG AL VD + TGS K++ A E MK Sbjct: 189 VAEILIEAGAPAGVFNVVQGMGE-VGGALVTDPRVDKVSLTGSVPTGKKVYAAAAEG-MK 246 Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMV 322 + +E GGKSP I+F DA D+ A A + ++ G+VC+ G+R+ V++ IK+KFL + Sbjct: 247 HVTMELGGKSPLIIFDDA-DIDNAVGGAINGNFYSSGQVCSNGTRVFVQKGIKEKFLARL 305 Query: 323 VEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTY 382 E G+P+D T+ G +V QMN VL YIE G ++GA+L+ GG+R + G + Sbjct: 306 AERTGNAILGDPMDEATSFGPMVTENQMNIVLGYIEKGKEEGARLICGGRRA--DMDGYF 363 Query: 383 VEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAH 442 +EPT+F VT+ M IA+EEIFGPV+SV+ FDT EE VA ANDT +GL+AG++T D ++AH Sbjct: 364 IEPTVFADVTDDMTIAREEIFGPVMSVLDFDTEEEVVARANDTEFGLSAGVFTKDFTRAH 423 Query: 443 KTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497 + + AGS ++N Y+ + APFGG K SG GR+ S A++ ++++K+ ++++ Sbjct: 424 RVIGNLEAGSCFINSYNDAPVEAPFGGVKASGVGRENSKEAIKHFSQVKSVYVRM 478 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: 589 Number of extensions: 27 Number of successful extensions: 6 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: 485 Length adjustment: 34 Effective length of query: 463 Effective length of database: 451 Effective search space: 208813 Effective search space used: 208813 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