Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate 5211158 Shew_3574 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__PV4:5211158 Length = 506 Score = 268 bits (685), Expect = 3e-76 Identities = 174/491 (35%), Positives = 252/491 (51%), Gaps = 32/491 (6%) Query: 10 RQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPAWRALTA 69 R +I G+W+ G+ +P G+V V + + A++AA A AW + Sbjct: 18 RYDNFIGGQWVAPVGGEYFDNRSPVDGQVFCQVARSDERDIELALDAAHAAKDAWGKTSV 77 Query: 70 KERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKG--------EIAYAASFIEWFAE 121 ERS L + + + +N + LA T E GK + E Y A I Sbjct: 78 TERSNLLLKIADRVEQNLEFLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEG 137 Query: 122 EAKRIYGDTIPGHQPDKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKP 181 A I +T+ H P+ P+GV I PWNFP M K PALAAG +VLKP Sbjct: 138 SAADIDNNTVSYHFPE--------PLGVVGQIIPWNFPLLMAAWKIAPALAAGNCIVLKP 189 Query: 182 ASQTPYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQL 241 A QTP S L +VEL +PAGVL++V G E G L + + KL+FTGST+IG + Sbjct: 190 AEQTPVSILVMVELIQDL-LPAGVLNIVNGFGTEAGQALAVSKRIAKLAFTGSTQIGHHI 248 Query: 242 MEECAKDIKKVSLELGGNAPFIVF------DDADLDKAVEGAIISKYRNNGQTCVCANRI 295 ++ A+ + ++ELGG +P I F +D LDKAVEG +++ + N G+ C C +R+ Sbjct: 249 LKCAAESLIPSTVELGGKSPNIYFADVMEQEDEYLDKAVEGMLLA-FFNQGEVCTCPSRV 307 Query: 296 YVQDGVYDAFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVL 355 + + +YD F +K+ A +K GN L+ T G + K+ ++E ++GA+VL Sbjct: 308 LIAESIYDKFIDKVIARAKTIKQGNPLDTDTQVGAQASQEQFDKILSYLEIGRNEGAEVL 367 Query: 356 SGGKLIE-------GNFFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDT 408 GG + G + EPTIL K V +EE FGP+ + FKDEAE +A++NDT Sbjct: 368 IGGTSCQLSGDQSSGFYIEPTILKGHNK-MRVFQEEIFGPVISVTTFKDEAEALAIANDT 426 Query: 409 EFGLASYFYARDMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIE 468 E+GL + + RDM+R R+ ++ G V IN A FGG K SG+GRE K + Sbjct: 427 EYGLGAGVWTRDMNRAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLS 486 Query: 469 DYLEIKYLCIS 479 Y K L +S Sbjct: 487 HYQNTKNLLVS 497 Lambda K H 0.317 0.134 0.384 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: 587 Number of extensions: 27 Number of successful extensions: 7 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: 480 Length of database: 506 Length adjustment: 34 Effective length of query: 446 Effective length of database: 472 Effective search space: 210512 Effective search space used: 210512 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