Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate H281DRAFT_02333 H281DRAFT_02333 aldehyde dehydrogenase (NAD+)
Query= BRENDA::Q72IB9 (516 letters) >FitnessBrowser__Burk376:H281DRAFT_02333 Length = 482 Score = 259 bits (661), Expect = 2e-73 Identities = 174/464 (37%), Positives = 238/464 (51%), Gaps = 15/464 (3%) Query: 41 YIGGEWVDTKERMVSLNPSAPSEVVGTTAKAGKAEAEAALEAAWKAFKTWKDWPQEDRSR 100 YI G W VSLNPS E VG +A + ++A+EAA AF+ W + R+ Sbjct: 17 YINGGWETGATTGVSLNPSDLDEPVGEYVRADVRQTDSAIEAASAAFREWALSSAQRRAD 76 Query: 101 LLLKAAALMRRRKRELEATLVYEVGKNWVEASADVAEAIDFIEYYARAALR-YRYPAVEV 159 L + M R+ EL L EVGK EA A+ A + A A R Y P Sbjct: 77 ALDAIGSEMLARRDELGRLLAREVGKTLPEALAEATRAGQTFKLLAADAQRAYAEPLASA 136 Query: 160 VPYPGEDNESFYVPLGAGVVIAPWNFPVAIFTGMIMGPVAVGNTVIAKPAEDAVVVGAKV 219 G + + PLG +IAPW+ P+AI G I +A GN V+ KPAE A + Sbjct: 137 --RAGVEIDMTREPLGVVGIIAPWSAPLAIAAGKIGAALAHGNCVVYKPAESTPACAAAL 194 Query: 220 FEIFHEAGFPPGVVNFLPGVGEEVGAYLVEHPRTRFINFTGSLEVGLKIYEAAGRLAPGQ 279 I AG P GV N + G G +VGA +V HP I+F+GS E G ++ +AA Sbjct: 195 ASIVSRAGLPAGVFNLVMGSGRQVGARIVAHPLVAAISFSGSAETGTRVLQAAAARQ--- 251 Query: 280 TWFKRAYVETGGKDAIIVDETADFDLAAEGVVVSAYGFQGQKCSAASRLILTQGAYEPVL 339 R +E GGK+ +V AD D A + + AYG GQ+ +AA+RLI+ + +EP + Sbjct: 252 ---ARVQLEMGGKNPFVVLADADLDSAVDAALTGAYGSTGQRSTAAARLIVERSIFEPFV 308 Query: 340 ERVLKRAERLSVGPA-EENPDLGPVVSAEQERKVLSYIEIGKNEG-QLVLGGKRLE--GE 395 + + + RL+V A + D+GPV +A Q + L Y+EIGK EG QL+ GG++LE Sbjct: 309 DALQTKLARLNVDHALKHGADMGPVANAAQLERDLDYVEIGKQEGAQLLHGGRQLERATR 368 Query: 396 GYFIAPTVFTEVPPKARIAQEEIFGPVLSVIRVKDFAEALEVANDTPYGLTGGVYSRKRE 455 GYF P +F P+ RIA+EEIFGP+ V+R D+ AL +ANDT YGL G+ +R Sbjct: 369 GYFFEPALFVG-EPEHRIAREEIFGPLAVVLRADDYDHALHLANDTAYGLCAGICTRSLS 427 Query: 456 HLEWARREFHVGNLYFNRKITGALVGVQPFGGFKLSGTNAKTGA 499 RR H G + N T A+ P GG K S + A Sbjct: 428 RARHFRRHVHSGLVTINLP-TSAVEHHAPGGGRKASAYGSTDAA 470 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: 538 Number of extensions: 20 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: 516 Length of database: 482 Length adjustment: 34 Effective length of query: 482 Effective length of database: 448 Effective search space: 215936 Effective search space used: 215936 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