Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate WP_011032002.1 MM_RS00260 aldehyde dehydrogenase
Query= BRENDA::Q72IB9 (516 letters) >NCBI__GCF_000007065.1:WP_011032002.1 Length = 492 Score = 318 bits (815), Expect = 3e-91 Identities = 194/483 (40%), Positives = 270/483 (55%), Gaps = 15/483 (3%) Query: 36 RHYPLYIGGEWVD--TKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDW 93 R Y L IGG+ VD T E +NP A E + T AG + + A+EAA F+ W + Sbjct: 3 REYKLLIGGKSVDSSTGETFDDINP-ATLENLATLQVAGIEDVDRAVEAAEAGFRVWSEV 61 Query: 94 PQEDRSRLLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALRYR 153 P R+ +L +AA +M+ RK L + E+GK E DV EAID I YA R Sbjct: 62 PAPGRAEVLFRAARIMQERKEGLARLMTEEMGKVLPETRGDVQEAID-ITIYAAGEGRRM 120 Query: 154 YPAVEVVPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAV 213 + + + P+G +I PWNFP+AI + IM + GN ++ KPA D Sbjct: 121 FGETTTSELRDKFCMTVLRPVGVVGMITPWNFPIAIPSWKIMPALIAGNAIVFKPASDTP 180 Query: 214 VVGAKVFEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAG 273 ++ K+ EI EAG PPGV+N +PG G G +V+HPR R I+FTGSL+ G I E Sbjct: 181 LLTIKLVEILMEAGLPPGVINIVPGPGGSTGKAIVQHPRIRAISFTGSLDTGKWIMEECA 240 Query: 274 RLAPGQTWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQG 333 + KR +E GGK+ +IV + A+ +LA EGVV A+G GQ+C+A SRLIL + Sbjct: 241 KS------MKRVSLELGGKNPVIVMDDANLELALEGVVWGAFGTTGQRCTATSRLILHEK 294 Query: 334 AYEPVLERVLKRAERLSVGPA-EENPDLGPVVSAEQERKVLSYIEIGKNEGQLVL-GGKR 391 + ++R+L + + L VG D+GPV++ Q K+ Y+ IGK EG +L GG R Sbjct: 295 IKDEFIKRLLAKTKSLRVGNGLLPETDVGPVINKAQLEKIEKYVRIGKEEGAAILVGGNR 354 Query: 392 LEG--EGYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGV 449 ++ GYF PT+FT+V P+ RIAQEEIFGPVLS+I V DF EA+EVAN+ YGL+ + Sbjct: 355 IDPGLPGYFFEPTIFTDVSPEMRIAQEEIFGPVLSIITVSDFDEAIEVANNIKYGLSSAI 414 Query: 450 YSRKREHLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGALDYLRLFLEM 509 Y+ A + G Y N GA V + PFGG K +G + + ++ F E+ Sbjct: 415 YTENVRTAFRAIEKLEAGITYVNAPTIGAEVHL-PFGGIKGTGNGFREAGTEAIKEFTEV 473 Query: 510 KAV 512 KAV Sbjct: 474 KAV 476 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: 609 Number of extensions: 39 Number of successful extensions: 6 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: 492 Length adjustment: 34 Effective length of query: 482 Effective length of database: 458 Effective search space: 220756 Effective search space used: 220756 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 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