Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate Ac3H11_1496 Aldehyde dehydrogenase (EC 1.2.1.3)
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1496 Length = 500 Score = 343 bits (879), Expect = 1e-98 Identities = 210/502 (41%), Positives = 283/502 (56%), Gaps = 11/502 (2%) Query: 1 MNFHHLAYWQDKALSLAIENRL--FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVD 58 MN L+ Q + E R+ I G A DP T+ +A+ + D Sbjct: 1 MNPFDLSSQQLQGAKFLSERRVGNVIGGVSGPALSGRWLPVTDPATEMVVAEAPDSDAAD 60 Query: 59 IDRAMSAARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLR 118 I RA+++A+ F+ W PA R+ +L +L++L+E HA+EL+ LETL +GK + Sbjct: 61 IARAVASAQRAFDSHVWRGLRPADREKLLFRLSELIERHADELSALETLQSGKLQGIARA 120 Query: 119 DDIPGAARAIRWYAEAIDKVYGEVATTS-----SHELAMIVREPVGVIAAIVPWNFPLLL 173 D+ A +R+ A K+ G+ S + REPVGV+ AIVPWNFPL + Sbjct: 121 IDVQAGAEFVRYMAGWATKLEGQTLDNSIPIPGPQWVTYTRREPVGVVGAIVPWNFPLAI 180 Query: 174 TCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSR 233 WK+ PALAAG +V+LKPSE +PL+A+RLA LA EAG+P+GVLNVV G G AG AL Sbjct: 181 ALWKIAPALAAGCTVVLKPSEDTPLTALRLAHLALEAGIPEGVLNVVCGRGATAGAALIA 240 Query: 234 HNDIDAIAFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAG 293 H + ++FTGST GK ++ A NM R LE GGKS +V D D Q A A G Sbjct: 241 HPGVRKLSFTGSTAVGK-VVGHAAVENMARFTLELGGKSPAVVMEDA-DPSQVAQGIATG 298 Query: 294 IFYNQGQVCIAGTRLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSV 353 IF++QGQVC A +RLL+ S+ L L AQ + G D AT G L AH V Sbjct: 299 IFFHQGQVCTASSRLLVHRSLYRRVLDELAGIAQGMRIGSGFDAATQFGPLTSKAHFARV 358 Query: 354 HSFIREGESKGQLLLDG--RNAGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSE 411 FI +++G L+ G R + PTIF D + REE+FGPVL V F Sbjct: 359 MDFIASAKAEGATLVAGGERVHDAGCFVQPTIFADTTAQMRVVREEVFGPVLAVAPFDDV 418 Query: 412 EQALQLANDSQYGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGN 471 E A+ AND+ YGL A++WT+ LS AHR+ RL+AG V+VN +N D +P GG KQSG Sbjct: 419 EDAIAAANDTPYGLAASLWTQSLSHAHRIVPRLQAGVVWVNAHNVLDAGLPLGGIKQSGT 478 Query: 472 GRDKSLHALEKFTELKTIWISL 493 GRD A+E FTELK++ +++ Sbjct: 479 GRDLGRAAVEGFTELKSVCMAV 500 Lambda K H 0.317 0.133 0.389 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: 581 Number of extensions: 28 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: 495 Length of database: 500 Length adjustment: 34 Effective length of query: 461 Effective length of database: 466 Effective search space: 214826 Effective search space used: 214826 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 (21.7 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