Align glutarate-semialdehyde dehydrogenase (EC 1.2.1.20) (characterized)
to candidate PfGW456L13_3737 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::Q88RC0 (480 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3737 Length = 496 Score = 351 bits (900), Expect = e-101 Identities = 191/480 (39%), Positives = 284/480 (59%), Gaps = 11/480 (2%) Query: 10 RQQAYINGEWLDADNGQTIKVTNPATGEVIGTVPKMGTAETRRAIEAADKALPA--WRAL 67 R +I+G+W+ A+ G +I V NPATG+ + RA++++ KA + W +L Sbjct: 17 RHGCFIDGQWVLAE-GDSIAVVNPATGQTLCETLDAPLELVERAVQSSHKAFKSGVWSSL 75 Query: 68 TAKERSAKLRRWFELMIENQDDLARLMTTEQGKPLAEAKG-EIAYAASFIEWFAEEAKRI 126 +R L + L+ E+ ++LA+L T QGK + A+ ++ F+ + + A +I Sbjct: 76 RPADRERILLNFTRLVEEHAEELAQLETLSQGKSINMARALDLNATVEFMRYMSGWATKI 135 Query: 127 YGDTIPGHQP-----DKRLIVIKQPIGVTAAITPWNFPAAMITRKAGPALAAGCTMVLKP 181 G T P ++P+GV I PWNFP + K PALA GCT+++KP Sbjct: 136 EGQTFDVSIPLPPGAKFTAFTKREPVGVVVGIVPWNFPLLIAAWKLMPALATGCTVIIKP 195 Query: 182 ASQTPYSALALVELAHRAGIPAGVLSVVTGSAGEVGGELTGNSLVRKLSFTGSTEIGRQL 241 A +TP +A+ L ELA AGIPAGV +VVTG VGG LT + LV K+SFTGST +G+ + Sbjct: 196 AMETPLTAMRLAELALEAGIPAGVFNVVTGGGASVGGVLTQHPLVSKVSFTGSTAVGKSV 255 Query: 242 MEECAKDIKKVSLELGGNAPFIVFDDADLDKAVEGAIISKYRNNGQTCVCANRIYVQDGV 301 C +++ + SLELGG P IV DAD++KAV+GAI+ NNGQ C A+R YV + Sbjct: 256 GVACMENMTRFSLELGGKNPMIVLADADIEKAVQGAILGGLLNNGQVCAAASRFYVHRSI 315 Query: 302 YDAFAEKLAAAVAKLKIGNGLEEGTTTGPLIDGKAVAKVQEHIEDAVSKGAKVLSGGKLI 361 +D F E LAAAV+ + IG G+ PL+ K V +HIE A +GA+V++GG+L+ Sbjct: 316 HDQFVEALAAAVSSMPIGAGMNCDAAINPLVSRKQQQSVLKHIELARQQGARVVTGGELL 375 Query: 362 EGN--FFEPTILVDVPKTAAVAKEETFGPLAPLFRFKDEAEVIAMSNDTEFGLASYFYAR 419 EG+ F +PTIL D+ + AVA+EE FGP+ + F DE VI ++ND +GLA+ + Sbjct: 376 EGDGFFVQPTILADIDHSMAVAREEVFGPVLGVMPFDDEDAVIELANDNRYGLAASLWTN 435 Query: 420 DMSRVFRVAEALEYGMVGINTGLISNEVAPFGGIKASGLGREGSKYGIEDYLEIKYLCIS 479 D+ + + +E G V +N ++ + PFGG+K SG+GRE + IE Y E+K +CI+ Sbjct: 436 DLGKAMNLVPRIEAGTVWVNAHVLLDPAMPFGGVKQSGMGREFGRAVIEAYTELKSVCIA 495 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: 561 Number of extensions: 29 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: 480 Length of database: 496 Length adjustment: 34 Effective length of query: 446 Effective length of database: 462 Effective search space: 206052 Effective search space used: 206052 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