Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF5142 PS417_26340 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__WCS417:GFF5142 Length = 490 Score = 367 bits (942), Expect = e-106 Identities = 192/479 (40%), Positives = 282/479 (58%), Gaps = 5/479 (1%) Query: 21 RAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAP 80 + +I+G YTDA S TFE ++P +G LA+V D RAV +A +W+ + Sbjct: 8 KLYIDGGYTDAGSDATFEAINPANGEVLAQVQRATKEDVERAVVSAEK--GQKIWAAMTA 65 Query: 81 AKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYD 140 +R L R D+LR+ +ELA LETLD GK ++ +DI A + + A + + Sbjct: 66 MERSRILRRAVDILRERNDELAALETLDTGKAFSETKYVDIVTGADVLEYYAGLVPAIEG 125 Query: 141 EVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTA 200 E P REP+GVV I WN+P+ +A WK PALA GN+++ KPSE + LT Sbjct: 126 EQIPLRDTSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLTT 185 Query: 201 IRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESN 260 +++A++ EAG+PAGV NVL G G VG L H ++ + FTG T K++M A S+ Sbjct: 186 LKLAEIYTEAGVPAGVFNVLTGSGREVGTWLTEHPRIEKVSFTGGTDTGKKVMASASSSS 245 Query: 261 MKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLP 320 +K + +E GGKSP IVF DA DL AA+ A A ++ G+VCT G+R+ V + ++ F Sbjct: 246 LKEVTMELGGKSPLIVFEDA-DLDRAADIAMMANFYSSGQVCTNGTRVFVPKHLQAAFEA 304 Query: 321 MVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTL--EET 378 +VE + + GNP D T G LV M +VL YI G ++GA++L GG R E Sbjct: 305 KIVERVARIRVGNPQDDNTNFGPLVSFAHMESVLGYIAKGKEEGARVLCGGDRLTDGEFA 364 Query: 379 GGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDI 438 G +V PT+F T+ M I +EEIFGPV+S++ ++T EE + ANDT +GLAAG+ T D+ Sbjct: 365 KGAFVAPTVFTDCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDTDFGLAAGLVTKDL 424 Query: 439 SKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497 ++AH+ + AG W+N + D P GG+KQSG GR+ + +L +T +K+ ++L Sbjct: 425 NRAHRVIHQLEAGICWINAWGESDAKMPVGGYKQSGVGRENGISSLNNFTRIKSVQVEL 483 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: 633 Number of extensions: 27 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: 490 Length adjustment: 34 Effective length of query: 463 Effective length of database: 456 Effective search space: 211128 Effective search space used: 211128 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