Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate AZOBR_RS22315 AZOBR_RS22315 aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__azobra:AZOBR_RS22315 Length = 497 Score = 301 bits (770), Expect = 5e-86 Identities = 181/490 (36%), Positives = 276/490 (56%), Gaps = 13/490 (2%) Query: 13 ALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFER 72 AL+ + ++ F GE+ A+ + F V+P T +A+ A G++ D+D A++AA V + Sbjct: 13 ALARELSSKHFFGGEFRPASSGKGFPVVNPATGETVAEAAFGEAADVDAAVAAA--VAAQ 70 Query: 73 GDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYA 132 +W+ +R ++ + +++AH EE+A L L+TGK +R R + + A ++ Sbjct: 71 KEWAKRPVRERGKLVAECGRVLDAHKEEIAKLIALETGKALRTESRVEAGVLSDAFVFFG 130 Query: 133 EAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKP 192 ++ GE + L M VREPVGV+ AI+PWN PLLL K+ PA+ AGN+V++K Sbjct: 131 GLAPELKGETIPFNPSMLTMTVREPVGVVGAIIPWNVPLLLMALKIAPAMVAGNAVVVKS 190 Query: 193 SEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQL 252 +E++PL+ +R+ L +P GV+N+++G+G E G L H D+ + FTGS TGK + Sbjct: 191 AEEAPLAVLRVVQLINTV-IPAGVVNILSGYGPECGAPLVAHKDVKKVTFTGSVETGKIV 249 Query: 253 LKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGI-FYNQGQVCIAGTRLLLE 311 K A + + V LE GGKS IV D DL QA + AG+ F QGQ C A +R+ + Sbjct: 250 YKTAAE-KLIPVTLELGGKSPMIVCGDA-DLDQAIAGAIAGMRFTRQGQSCTASSRIFVH 307 Query: 312 ESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKG------Q 365 +SI D F+ LK++ + G PLD +T +GT++ D V S+I G+ G Sbjct: 308 DSIHDAFVEKLKEKVNAMKMGDPLDESTDIGTIVSPQQLDRVQSYIAIGKEGGATPHVCS 367 Query: 366 LLLDGRNAGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGL 425 + + P IF V + +++EEIFGPV V R+T E+ + AND++YGL Sbjct: 368 AMPSDPKLTKGLYVQPHIFTGVKNSDRIAQEEIFGPVCCVIRWTDYEEVIAQANDTEYGL 427 Query: 426 GAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHA-LEKFT 484 A +WTRDL A RL+AG V VN + +GG K SG G++ SL A LE FT Sbjct: 428 AATIWTRDLKVAMDAVHRLEAGFVQVNQNLVVQPNLSYGGVKSSGLGKEASLEAMLEHFT 487 Query: 485 ELKTIWISLE 494 KTI I+++ Sbjct: 488 HKKTIIINMK 497 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: 557 Number of extensions: 26 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: 495 Length of database: 497 Length adjustment: 34 Effective length of query: 461 Effective length of database: 463 Effective search space: 213443 Effective search space used: 213443 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