Align 1-pyrroline-5-carboxylate dehydrogenase 2; P5C dehydrogenase 2; EC 1.2.1.88; L-glutamate gamma-semialdehyde dehydrogenase (uncharacterized)
to candidate HSERO_RS07235 HSERO_RS07235 aldehyde dehydrogenase
Query= curated2:Q9K5Z5 (515 letters) >FitnessBrowser__HerbieS:HSERO_RS07235 Length = 477 Score = 249 bits (635), Expect = 2e-70 Identities = 156/484 (32%), Positives = 246/484 (50%), Gaps = 15/484 (3%) Query: 35 KDYPLVINGERVTTDD--KIVSVNPAMKEQVIGVVSKASREIVDDAFKSAETAFHTWKNV 92 KD L INGE + I +NPA E+VIG ++ A R +D A ++A F TW+N+ Sbjct: 3 KDVQLFINGEWTASASGRTIDVINPAT-EEVIGKIAHADRADLDRALEAASKGFETWRNM 61 Query: 93 NPEERANILIRAAAIIRRRKHEFSAWLVKEAGKPWKEADADTAEAIDFLEYYARQMITLK 152 + ER+ I+ RAA ++R R E + + E GKP EA +T A D ++++A + Sbjct: 62 SAFERSKIMRRAADLLRERAEEVARLMTMEQGKPLAEAKMETLGAADTIDWFAEEARRTY 121 Query: 153 DGKPVNSR-EGEHNRYFYTPIGVCVTISPWNFALAIMAGTTVAPIVTGNTVLLKPASTTP 211 G+ V +R G + P+G +PWNF L + A + G ++++K TP Sbjct: 122 -GRLVPARVPGAYQMVIKEPVGPVAAFTPWNFPLNQVVRKLSAALAAGCSIIVKAPEETP 180 Query: 212 VVAAKFVEVLEEAGLPKGVVNFVPGSGTDIGDYLIDHPKTSLITFTGSRDVGVRLYERAA 271 A+ + +AG+P GV+N V G +I +YLI HP I+FTGS VG +L A Sbjct: 181 ASPAELIRAYADAGVPAGVINLVYGVPAEISEYLIPHPVIKKISFTGSTPVGKQLAALAG 240 Query: 272 VVHPGQQHLKRVIVEMGGKDTVVVDKDADLDLAAQSIVTSAFGFSGQKCSAGSRAVIHQD 331 QH+KR +E+GG +V DAD+D+AA+ + T+ F +GQ C + +R ++ + Sbjct: 241 ------QHMKRATMELGGHAPAMVFDDADVDVAAKMLATAKFRNAGQVCVSPTRFLVQKG 294 Query: 332 VYDVVLEKAVALTKQLSVGEPTAPDVYMGPVVDQGAFSKIMSYIEVGKEEG-RLMVGGEG 390 V++ ++K V +QL VG + MGPV ++ + + I+ +G +L GG+ Sbjct: 295 VFNAFVDKFVTYAEQLKVGNGLEAGITMGPVANKRRIPALEALIDDAVSQGAQLRTGGKR 354 Query: 391 DDSKGFFIQPTIFADVDPHARIMQEEIFGPVVAFSKARDFDHALEIANNTEYGLTGAVIT 450 +KG+F QPT+ ++ AR M EE FGP+ + D + AN YGL Sbjct: 355 IGNKGYFFQPTVLTNLPLQARAMNEEPFGPLALINSFETLDEVITEANRLPYGLAAYAFA 414 Query: 451 TNRHHIEKAKRDFHVGNLYFNRNCTGAIVGYHPFGGFKMSGTDSKAGGPDYLALHMQAKT 510 + H G L N G + PFGG K SG S+ GG + + ++ K Sbjct: 415 KSAHTKHALAARVESGMLTINH--LGLALPELPFGGIKDSGYGSE-GGTEAIEAYINTKL 471 Query: 511 VSEM 514 V+++ Sbjct: 472 VTQL 475 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: 532 Number of extensions: 17 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: 477 Length adjustment: 34 Effective length of query: 481 Effective length of database: 443 Effective search space: 213083 Effective search space used: 213083 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