Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate WP_066921795.1 ACG33_RS12920 aldehyde dehydrogenase family protein
Query= curated2:Q9K5Z5 (515 letters) >NCBI__GCF_001579945.1:WP_066921795.1 Length = 478 Score = 253 bits (647), Expect = 8e-72 Identities = 163/455 (35%), Positives = 238/455 (52%), Gaps = 34/455 (7%) Query: 55 VNPAMKEQVIGVVSKASREIVDDAFKSAETAFHTWKNVNPEERANILIRAAAIIRRRKHE 114 ++PA E IG + + E VD A ++ TAF TW+ EER + R R R E Sbjct: 25 IDPAT-ETAIGKILLGTPEDVDAAVRAGRTAFATWQQTTREERIELFERIIEAYRARTQE 83 Query: 115 FSAWLVKEAGKPWKEADADTAEAIDFLEYYARQMITLKD-------GKPVNSREGEHNRY 167 +A + E G P + A A+A L ++ + LKD G + RE Sbjct: 84 MAAAISDEMGAPMRFALR--AQAASGLGHFGAVLAVLKDFEFEESIGSTLIRRE------ 135 Query: 168 FYTPIGVCVTISPWNFALAIMAGTTVAPIVTGNTVLLKPASTTPVVAAKFVEVLEEAGLP 227 PIGVC I+PWN+ + ++ A + G T++LKP+ P+ A F E+L EAG+P Sbjct: 136 ---PIGVCGLITPWNWPINQISCKVAAALAAGCTIVLKPSEIAPISAHLFTEILVEAGVP 192 Query: 228 KGVVNFVPGSGTDIGDYLIDHPKTSLITFTGSRDVGVRLYERAAVVHPGQQHLKRVIVEM 287 KGV N + G GT +G + HP +++FTGS GV++ + AA +KRV E+ Sbjct: 193 KGVFNLIDGEGTTVGAAISRHPDIDMVSFTGSTRAGVQVAKAAA------DTVKRVSQEL 246 Query: 288 GGKDTVVVDKDADLDLAAQSIVTSAFGFSGQKCSAGSRAVIHQDVYDVVLEKAVALTKQL 347 GGK ++ +DADLD A + V + +GQ C+A SR ++ VYD + A A Q Sbjct: 247 GGKSANIILEDADLDAAVKDGVRAMMVNTGQSCNAPSRMLVPARVYDKAVAIAKAAAGQP 306 Query: 348 SVGEPTAPDVYMGPVVDQGAFSKIMSYIEVGKEEGRLMVGG-----EGDDSKGFFIQPTI 402 +G P A MGPV ++ F KI ++ G +EG +V G EG + KG+F++PTI Sbjct: 307 VIGNPKADGTTMGPVSNRRQFEKIQCLLQQGLDEGATLVAGGLGRPEGLE-KGYFVKPTI 365 Query: 403 FADVDPHARIMQEEIFGPVVAFSKARDFDHALEIANNTEYGLTGAVITTNRHHIEKAKRD 462 FADV I +EEIFGPV+ +D + A+ +AN+T YGL+G V + +R H + R Sbjct: 366 FADVRNDMTIAREEIFGPVLVMIPYQDEEEAVRMANDTIYGLSGYVYSGDREHARRIARR 425 Query: 463 FHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAG 497 VG ++ N T PFGG+K SG + G Sbjct: 426 LRVGMVHLNGAPTDIDA---PFGGYKQSGNGREWG 457 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: 550 Number of extensions: 19 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: 478 Length adjustment: 34 Effective length of query: 481 Effective length of database: 444 Effective search space: 213564 Effective search space used: 213564 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 24 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