Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF2074 PGA1_c21070 betaine aldehyde dehydrogenase BetB
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__Phaeo:GFF2074 Length = 488 Score = 313 bits (801), Expect = 1e-89 Identities = 191/478 (39%), Positives = 265/478 (55%), Gaps = 13/478 (2%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 +I G ++D + FE P G A + +D AV ARA F++ W+ + Sbjct: 7 YIGGVFSDGSA--RFESRDPASGEVWAMMPEARASDVEAAVAAARAAFHAPDWAGMTATG 64 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R L R ADL+ +N E LA LET D GK I ++S+ I A + A DK+ E Sbjct: 65 RGKLLYRLADLIAENAETLAQLETRDTGKIIRETSA-QIAYVADYYRYYAGLADKI--EG 121 Query: 143 APTPHDQLGL---VTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLT 199 A P D+ + + REP+GVV A+VPWN L +A K+GPALA G +VVLK SE++P Sbjct: 122 AHLPIDKPDMEVWLRREPLGVVAAVVPWNSQLFLAAVKIGPALAAGCTVVLKASEEAPAP 181 Query: 200 AIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGES 259 + A++ +AG P GVLNV+ G+G G L H +D + FTG A+ ++ + E Sbjct: 182 LLEFARIFDQAGFPRGVLNVITGFGADCGAVLTAHPGIDHIAFTGGPDTARHVVRNSAE- 240 Query: 260 NMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFL 319 N+ LE GGKSP IVF D D+ +A A SAI G+ C AGSRL++ IK +FL Sbjct: 241 NLASTSLELGGKSPFIVFEDV-DIDSAVNAQVSAIFAATGQSCVAGSRLIISNQIKAQFL 299 Query: 320 PMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETG 379 + E + + G P P+T VG L QM + + A GA+++ GG+ E Sbjct: 300 HRLKEKAENIRIGAPELPETEVGPLCTDAQMRRAVELVAASLAAGARIVTGGQPL--EGE 357 Query: 380 GTYVEPTIFD-GVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDI 438 G + PTI D +EE FGPVLSV FDT EA+A+ANDT +GLA+G++T D+ Sbjct: 358 GNFFPPTILDCSEAPEAPCLREEFFGPVLSVCGFDTEAEALALANDTAHGLASGVFTRDL 417 Query: 439 SKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIK 496 ++AH+ R +RAG VWVN Y APFGG SG+GR+ L A YT +K W++ Sbjct: 418 TRAHRMIRGIRAGIVWVNTYRAVSPIAPFGGQGLSGHGREGGLQAALDYTRVKTVWLR 475 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: 572 Number of extensions: 29 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: 488 Length adjustment: 34 Effective length of query: 463 Effective length of database: 454 Effective search space: 210202 Effective search space used: 210202 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