Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate Pf1N1B4_2417 Betaine aldehyde dehydrogenase (EC 1.2.1.8)
Query= BRENDA::Q9RW56 (523 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2417 Length = 490 Score = 228 bits (582), Expect = 3e-64 Identities = 157/491 (31%), Positives = 238/491 (48%), Gaps = 33/491 (6%) Query: 42 LIIDG--QEVDTEGKIQSINPCDTSEVVGTTAKATIGDAENALQGAWKAFESWKKWDMDA 99 L IDG + ++ ++INP + EV+ T +AT D E A+ A K + W Sbjct: 9 LYIDGGYSDASSDATFEAINPAN-GEVLATVQRATKEDVERAVVSAEKGQKIWAAMTAME 67 Query: 100 RARILLKAAAILKRRRLEACALMSIEVGKNYAEAD-VEVAEAIDFLEYYARSAMKYAGFG 158 R+RIL +A IL+ R E AL +++ GK Y+E V++ D LEYYA Sbjct: 68 RSRILRRAVDILRERNDELAALETLDTGKAYSETRYVDIVTGADVLEYYAGLVPA----- 122 Query: 159 SSETTWFEGEENGLMSI--------PLGVGVSISPWNFPCAIFVGMAAAPIVAGNCVVVK 210 EGE+ L + PLG+ I WN+P I + +A + AGN ++ K Sbjct: 123 ------IEGEQIPLRTTSFVYTRREPLGIVAGIGAWNYPIQIALWKSAPALAAGNAMIFK 176 Query: 211 PAEDAGLIAGFMVDILREAGLPAGVLQFLPGVGKEVGEYLTTHAKTRFITFTGSRAVGLH 270 P+E L + +I EAGLPAGV L G G+EVG +LT H + I+FTG G Sbjct: 177 PSEVTSLTTLKLAEIYTEAGLPAGVFNVLTGSGREVGTWLTEHPRIEKISFTGGTDTGKK 236 Query: 271 INEVAAKVQPGQKWIKRVIMELGGKDGLIVDETADIENAITAATQGAFGFNGQKCSAMSR 330 + A+ +K V MELGGK LI+ + AD++ A A F +GQ C+ +R Sbjct: 237 VMASASGSS-----LKDVTMELGGKSPLIIFDDADLDRAADTAMMANFYSSGQVCTNGTR 291 Query: 331 LIVVDSVYDEVVNGFVERAKALKMGTGE-ENANVTAVVNQMSFNKIKGYLELAPSEG-KV 388 + V + VER +++G E EN N +V+ + GY+ EG ++ Sbjct: 292 VFVPSHLKAAFEAKIVERVARIRVGNPEDENTNFGPLVSFAHMESVLGYIAKGKEEGARL 351 Query: 389 LLGGEATGEANGKQGYYIQPTIVGDVDRNSRLAQEEIFGPVVAVLRAKDWQDALDIANST 448 L GG+ + +G ++ PT+ D + +EEIFGPV+++L + ++ + AN T Sbjct: 352 LCGGDRLTDGEFAKGAFVAPTVFTDCTDEMTIVREEIFGPVMSILTYETEEEVIRRANDT 411 Query: 449 EYGLTGGVCSNSRERLEQARAEFEVGNLYFNRKITGAIVGVQPFGGYNMSGTDSKAGGPD 508 E+GL GV + R + + E G + N G P GGY SG + G Sbjct: 412 EFGLAAGVVTKDLNRAHRVIHQLEAGICWIN--AWGESDAKMPVGGYKQSGV-GRENGIS 468 Query: 509 YLSNFMQLKTV 519 L+NF ++K+V Sbjct: 469 SLNNFTRIKSV 479 Lambda K H 0.317 0.134 0.391 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: 636 Number of extensions: 30 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: 523 Length of database: 490 Length adjustment: 34 Effective length of query: 489 Effective length of database: 456 Effective search space: 222984 Effective search space used: 222984 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