Align L-glutamate gamma-semialdehyde dehydrogenase (EC 1.2.1.88) (characterized)
to candidate RR42_RS11330 RR42_RS11330 aldehyde dehydrogenase
Query= BRENDA::P30038 (563 letters) >FitnessBrowser__Cup4G11:RR42_RS11330 Length = 477 Score = 162 bits (410), Expect = 3e-44 Identities = 139/461 (30%), Positives = 221/461 (47%), Gaps = 50/461 (10%) Query: 105 AIEAALAARKEWDLKPIADRAQIFLKAADMLSGPRRAEILAKTMVGQ-GKTVIQAEI--- 160 AI+AA AA W P + RA K A+ L R+E LA+ + G+ G + A Sbjct: 47 AIQAARAAFDSWSATPPSVRAGYIRKIAEGLKA--RSEELAQLIAGEVGMPIKMARAIQV 104 Query: 161 -------DAAAELIDFFRFNAKYAVELEGQQPISVPPSTNSTVYRGLEGFVAAISPFNFT 213 AA+L+D F F + NS V R G VAAI+P+N+ Sbjct: 105 GGPVYNWAQAAKLLDTFAFEEEVG---------------NSLVVREPVGVVAAITPWNYP 149 Query: 214 AIGGNLAGAPALM-GNVVLWKPSDTAMLASYAVYRILREAGLPPNIIQFVPADGPLFGDT 272 L APAL G V+ KPS+ A L ++ + ++ AGLPP + V GP+ G+ Sbjct: 150 LNQITLKVAPALAAGCTVVLKPSEVAPLNAFVLAEVIEAAGLPPGVFNLVTGYGPVVGEV 209 Query: 273 VTSSEHLCGINFTGSVPTFKHLWKQVAQNLDRFHTFPRLAGECGGKNFHFVHRSADVESV 332 + S + ++FTGS K + + AQ++ R+A E GGK+ + AD+ + Sbjct: 210 LASHPEVDMVSFTGSTRAGKRVSELGAQSV------KRVALELGGKSASVILDDADLAAA 263 Query: 333 VSGTLRSAFEYGGQKCSACSRLYVPHSLWPQIKGRLLEEHSRIKVGDPAEDFGTFFSAVI 392 V GT+ + F GQ CSA +R+ VP + + ++K + VGDP + + +I Sbjct: 264 VKGTVGACFLNSGQTCSAHTRMLVPRARYDEVKAIARKVVEGYTVGDPLLE-SSRLGPLI 322 Query: 393 DAKSFARIKKWLEHARSSPSLTILAGGKCDDSV--GYFVEPCIVESKDPQEPIMKEEIFG 450 A R+ +++ + + + G + + + G+FV+P ++ + DP+ + +EEIFG Sbjct: 323 SAAQKDRVTGYIQRGINEGAELVAGGPEAPEGLDKGFFVKPTVLGNVDPKATVAQEEIFG 382 Query: 451 PVLSVYVYPDDKYKETLQLVDSTTSYGLTGAVFSQDKDVVQEATKVLRN-AAGNFYINDK 509 PVLS+ Y D ++ +++ + + YGL G V+S D+ A +V R G IN Sbjct: 383 PVLSIICY--DTEEDAVRIANDSI-YGLGGGVWSGDE---ARAIRVARRIRTGQVDING- 435 Query: 510 STGSIVGQQPFGGARASGTNDKPG--GPHYILRWTSPQVIK 548 G Q PFGG + SG + G G L + S Q+ K Sbjct: 436 --GPFNMQAPFGGYKQSGNGREAGKYGLEEFLEYKSLQMKK 474 Lambda K H 0.319 0.135 0.411 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: 657 Number of extensions: 35 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: 563 Length of database: 477 Length adjustment: 35 Effective length of query: 528 Effective length of database: 442 Effective search space: 233376 Effective search space used: 233376 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