Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate HSERO_RS11260 HSERO_RS11260 aldehyde dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >FitnessBrowser__HerbieS:HSERO_RS11260 Length = 477 Score = 241 bits (615), Expect = 4e-68 Identities = 169/484 (34%), Positives = 247/484 (51%), Gaps = 22/484 (4%) Query: 41 YIGGEWV--DTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFK-TWKDWPQED 97 +I WV + E + L+PS + A+ + + A+ AA A++ W + Sbjct: 5 FIANRWVAPTSGESIPVLDPS-DGQPFDAIARGNATDIDQAVRAARLAYEGAWGRLSAAE 63 Query: 98 RSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYRYPAV 157 RSRLL+K A ++ + EL + GK +A AD A + + E+YA AA + Sbjct: 64 RSRLLMKLAYKLQDHQEELAQLEGRDCGKPMKQARADAAAIVRYFEFYAGAADKLHG--- 120 Query: 158 EVVPYP-GEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVG 216 + +PY G + P G I PWN+P+ IF + G +A GNT + KPAEDA + Sbjct: 121 DTIPYQAGYTVLTLREPHGVTGHIVPWNYPMQIFGRCVGGALAAGNTCVVKPAEDACLSI 180 Query: 217 AKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLA 276 +V E+ E GFP G +N + G G E G LV+HP I+FTGS VG + AA Sbjct: 181 LRVAELAAEVGFPEGALNIVTGYGHEAGDLLVKHPDVNHISFTGSPNVGKLVVRAAAEHH 240 Query: 277 PGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYE 336 T +E GGK IV E AD + VV + GQ CSA SRL++ +GAYE Sbjct: 241 TPVT------LELGGKSPQIVFEDADMEAMLPVVVNAIVQNAGQTCSAGSRLLVQRGAYE 294 Query: 337 PVLERVLKRAERLSVGPAEENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRLEG- 394 VLER+ +L VG ++ + D GP++ Q+ +V ++ + +G L GK G Sbjct: 295 QVLERLSGLFSQLQVGSSQMDLDCGPLIRKTQQERVAGFLSDAQRDGIALAAQGKIAAGV 354 Query: 395 --EGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSR 452 G++ AP + +VPP+ R+AQEE+FGPVL+ + +D A A+ +AN T YGL V++R Sbjct: 355 PTGGFYQAPALLRDVPPRHRLAQEEVFGPVLAAMPFEDEAHAIALANGTDYGLVASVWTR 414 Query: 453 KREHLEWARREFHVGNLYFNRKITGALVGVQ-PFGGFKLSGTNAKTGALDYLRLFLEMKA 511 R G ++ N GA GV+ PFGG K SG + G + L F +K Sbjct: 415 DGGRQMRLARAIRSGQVFINN--YGAGGGVELPFGGVKASGHGREKG-FEALYGFTVLKT 471 Query: 512 VAER 515 +A R Sbjct: 472 IAIR 475 Lambda K H 0.319 0.137 0.403 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: 566 Number of extensions: 30 Number of successful extensions: 4 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: 516 Length of database: 477 Length adjustment: 34 Effective length of query: 482 Effective length of database: 443 Effective search space: 213526 Effective search space used: 213526 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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