Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate GFF2584 Psest_2634 glycine betaine aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__psRCH2:GFF2584 Length = 490 Score = 361 bits (926), Expect = e-104 Identities = 195/477 (40%), Positives = 280/477 (58%), Gaps = 5/477 (1%) Query: 23 FINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAK 82 +I+G Y DA S ETFE ++P +G LA+VA AD RAVE+A +W+ L + Sbjct: 10 YIHGGYVDASSNETFESINPANGEVLAQVAEAGAADLERAVESAEQ--GQRIWAALTGIE 67 Query: 83 RKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEV 142 R + R DLLR+ +ELALLETLD GKP+ ++ S+DI A + + A + E Sbjct: 68 RARIMRRAVDLLRERNDELALLETLDTGKPLSETRSVDIVTGADVLEYYAGLAPAIEGEQ 127 Query: 143 APTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 202 P REP+GVV I WN+P+ +A WK PALA GN+++ KPSE + L+A++ Sbjct: 128 IPLRDSSFVYTRREPLGVVAGIGAWNYPIQIALWKAAPALAAGNAMIFKPSEVTSLSALK 187 Query: 203 IAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMK 262 +A++ EAG+P GV NVL G G VG + H + + FTG K++M A S++K Sbjct: 188 LAEIFSEAGLPDGVFNVLTGSGAGVGALITEHPRIAKVSFTGGVATGKKVMASAASSSLK 247 Query: 263 RIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMV 322 + +E GGKSP I+ DA DL AA+ A A F+ G+VCT G+R+ V +K F + Sbjct: 248 DVTMELGGKSPLIICEDA-DLDRAADIAVMANFFSSGQVCTNGTRVFVPAGLKAAFEAKL 306 Query: 323 VEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTL--EETGG 380 +E ++ + G+P +T G LV MN VL YI G GA+LL GG+R E G Sbjct: 307 LERVQRIRLGDPQQEETNFGPLVSFAHMNNVLDYIAKGKAAGARLLCGGERVTEGEYAKG 366 Query: 381 TYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISK 440 +V PTIF ++ M I EEIFGPVLS++ + +E + ANDT YGLAAG+ T+D+++ Sbjct: 367 AFVAPTIFSDCSDDMAIVCEEIFGPVLSLLEYQDEDEVIRRANDTEYGLAAGVVTADLAR 426 Query: 441 AHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497 AH+ + AG W+N + P GG+KQSG GR+ + +L YT +K+ ++L Sbjct: 427 AHRIIHRLEAGICWINTWGESPAQMPVGGYKQSGIGRENGIASLAHYTRVKSVQVEL 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: 605 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