Align 4-guanidinobutyraldehyde dehydrogenase (EC 1.2.1.54) (characterized)
to candidate BPHYT_RS29875 BPHYT_RS29875 betaine-aldehyde dehydrogenase
Query= metacyc::MONOMER-11560 (497 letters) >FitnessBrowser__BFirm:BPHYT_RS29875 Length = 483 Score = 406 bits (1043), Expect = e-117 Identities = 218/474 (45%), Positives = 297/474 (62%), Gaps = 6/474 (1%) Query: 24 INGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENARATFNSGVWSQLAPAKR 83 I+G+ +GE ++P +A VA AD + AV ARA VW+ + A+R Sbjct: 14 IDGKRLPPGTGEYSVDINPATEEPIALVAQGSAADVDTAVRAARAALK--VWNGIRTAER 71 Query: 84 KAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQAIHWTAEAIDKVYDEVA 143 L+R A L+R N+EELA LE+LD GKPI DIP A + + A DK+ +V Sbjct: 72 ARILMRLAGLMRANLEELAALESLDAGKPIAAVMRQDIPAAIDTLEYYAGWCDKINGQVV 131 Query: 144 PTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIRI 203 P D L REPVGVV AIVPWNFPL++ WK+ PALA G ++++KP+E +PLTA+RI Sbjct: 132 PVRPDALTYTLREPVGVVAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITPLTALRI 191 Query: 204 AQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMVYAGESNMKR 263 +LA+EAG+P GVLN++ G G VG AL H VD + FTGS + + ++ A N KR Sbjct: 192 GELALEAGVPPGVLNIVTGKGRVVGDALVAHPGVDKVTFTGSPSVGRGILQGAA-GNFKR 250 Query: 264 IWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGSRLLVERSIKDKFLPMVV 323 + LE GGKS N++F DA +L A AAAS I FN G+VC+AGSR+L R + D+ + + Sbjct: 251 VTLELGGKSANLIFPDA-NLDNAVRAAASGIFFNTGQVCSAGSRILAHRDVYDEVVERLA 309 Query: 324 EALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAKLLAGGKRTLEETGGTYV 383 K K G+P +T++G L+ QM TVL Y+E G +GA L+ GG R E G +V Sbjct: 310 ARAKSIKVGDPSSRETSMGPLISAAQMKTVLGYVETGRAEGASLVTGGARVGER--GFFV 367 Query: 384 EPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTPYGLAAGIWTSDISKAHK 443 EPT+F V + MRI+QEEIFGPV SVI F+ +A+ IAN T Y LAAG+W++DI + H+ Sbjct: 368 EPTVFANVEHEMRISQEEIFGPVASVIRFNDEADAIRIANGTLYSLAAGVWSADIGRVHR 427 Query: 444 TARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEKYTELKATWIKL 497 AR +RAG+VW+N Y D+ P+GG SG GR+ A+E +TE KA W+ + Sbjct: 428 VARDLRAGTVWINTYGYTDVRLPWGGSGDSGFGREHGDVAIENFTEPKAVWLAI 481 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: 638 Number of extensions: 28 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: 483 Length adjustment: 34 Effective length of query: 463 Effective length of database: 449 Effective search space: 207887 Effective search space used: 207887 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