Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate BPHYT_RS29875 BPHYT_RS29875 betaine-aldehyde dehydrogenase
Query= curated2:Q9K5Z5 (515 letters) >FitnessBrowser__BFirm:BPHYT_RS29875 Length = 483 Score = 279 bits (714), Expect = 1e-79 Identities = 171/469 (36%), Positives = 251/469 (53%), Gaps = 22/469 (4%) Query: 37 YPLVINGERVT--TDDKIVSVNPAMKEQVIGVVSKASREIVDDAFKSAETAFHTWKNVNP 94 + L+I+G+R+ T + V +NPA +E I +V++ S VD A ++A A W + Sbjct: 10 HDLLIDGKRLPPGTGEYSVDINPATEEP-IALVAQGSAADVDTAVRAARAALKVWNGIRT 68 Query: 95 EERANILIRAAAIIRRRKHEFSAWLVKEAGKPWKEA-DADTAEAIDFLEYYARQMITLKD 153 ERA IL+R A ++R E +A +AGKP D AID LEYYA + + Sbjct: 69 AERARILMRLAGLMRANLEELAALESLDAGKPIAAVMRQDIPAAIDTLEYYAGWCDKI-N 127 Query: 154 GKPVNSREGEHNRYFYTPIGVCVTISPWNFALAIMAGTTVAPIVTGNTVLLKPASTTPVV 213 G+ V R P+GV I PWNF L I + G T+++KPA TP+ Sbjct: 128 GQVVPVRPDALTYTLREPVGVVAAIVPWNFPLMIGMWKIAPALACGCTLIVKPAEITPLT 187 Query: 214 AAKFVEVLEEAGLPKGVVNFVPGSGTDIGDYLIDHPKTSLITFTGSRDVGVRLYERAAVV 273 A + E+ EAG+P GV+N V G G +GD L+ HP +TFTGS VG + + AA Sbjct: 188 ALRIGELALEAGVPPGVLNIVTGKGRVVGDALVAHPGVDKVTFTGSPSVGRGILQGAA-- 245 Query: 274 HPGQQHLKRVIVEMGGKDTVVVDKDADLDLAAQSIVTSAFGFSGQKCSAGSRAVIHQDVY 333 + KRV +E+GGK ++ DA+LD A ++ + F +GQ CSAGSR + H+DVY Sbjct: 246 ----GNFKRVTLELGGKSANLIFPDANLDNAVRAAASGIFFNTGQVCSAGSRILAHRDVY 301 Query: 334 DVVLEKAVALTKQLSVGEPTAPDVYMGPVVDQGAFSKIMSYIEVGKEEG-RLMVGGEGDD 392 D V+E+ A K + VG+P++ + MGP++ ++ Y+E G+ EG L+ GG Sbjct: 302 DEVVERLAARAKSIKVGDPSSRETSMGPLISAAQMKTVLGYVETGRAEGASLVTGGARVG 361 Query: 393 SKGFFIQPTIFADVDPHARIMQEEIFGPVVAFSKARDFDHALEIANNTEYGLTGAVITTN 452 +GFF++PT+FA+V+ RI QEEIFGPV + + D A+ IAN T Y L V + + Sbjct: 362 ERGFFVEPTVFANVEHEMRISQEEIFGPVASVIRFNDEADAIRIANGTLYSLAAGVWSAD 421 Query: 453 RHHIEKAKRDFHVGNLYFNRNCTGAIVGYH----PFGGFKMSGTDSKAG 497 + + RD G ++ N GY P+GG SG + G Sbjct: 422 IGRVHRVARDLRAGTVWIN------TYGYTDVRLPWGGSGDSGFGREHG 464 Lambda K H 0.318 0.135 0.394 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: 578 Number of extensions: 23 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: 515 Length of database: 483 Length adjustment: 34 Effective length of query: 481 Effective length of database: 449 Effective search space: 215969 Effective search space used: 215969 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 (21.7 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