Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate PP_5278 PP_5278 4-guanidinobutyraldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Putida:PP_5278 Length = 497 Score = 570 bits (1469), Expect = e-167 Identities = 288/491 (58%), Positives = 354/491 (72%), Gaps = 4/491 (0%) Query: 7 AYWQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAA 66 A W+ +A L IE R FINGEYT A ETFE + PV LAK+A D +RA+ A Sbjct: 7 ADWEQRAQQLKIEGRAFINGEYTDAVSGETFECLSPVDGRFLAKVASCDLADANRAVENA 66 Query: 67 RGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAAR 126 R F G WS +PAKRKA L + ADL+ + EELALLETLD GKPI S DIPGAA+ Sbjct: 67 RATFNSGVWSQLAPAKRKAKLIRFADLLRKNVEELALLETLDMGKPIGDSSSIDIPGAAQ 126 Query: 127 AIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGN 186 AI W AEAIDKVY EVA T +L ++ REPVGV+ AIVPWNFPLL+ CWKLGPALA GN Sbjct: 127 AIHWTAEAIDKVYDEVAPTPHDQLGLVTREPVGVVGAIVPWNFPLLMACWKLGPALATGN 186 Query: 187 SVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGST 246 SV+LKPSEKSPL+AIR+A LA EAG+P GVLNV+ G+GH G+AL+ H D+D + FTGST Sbjct: 187 SVVLKPSEKSPLTAIRIAQLAIEAGIPAGVLNVLPGYGHTVGKALALHMDVDTLVFTGST 246 Query: 247 RTGKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGT 306 + KQL+ AG+SNMKR+WLEAGGKS NIVFAD PDLQ AA A A+ I +NQG+VC AG+ Sbjct: 247 KIAKQLMVYAGESNMKRIWLEAGGKSPNIVFADAPDLQAAAEAAASAIAFNQGEVCTAGS 306 Query: 307 RLLLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQL 366 RLL+E SI D+FL ++ + + W+PG+PLDP TT+G L+D ++V S+I G G Sbjct: 307 RLLVERSIKDKFLPMVVEALKGWKPGNPLDPQTTVGALVDTQQMNTVLSYIEAGHKDGAK 366 Query: 367 LLDGRNAGLAAAIG----PTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQ 422 LL G L G PTIF V +++EEIFGPVL V F + E+A+ +AND+ Sbjct: 367 LLAGGKRTLEETGGTYVEPTIFDGVTNAMRIAQEEIFGPVLSVIAFDTAEEAVAIANDTP 426 Query: 423 YGLGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEK 482 YGL A +WT D+S+AH+ +R ++AGSV+VN Y+ GDMT PFGG+KQSGNGRDKSLHALEK Sbjct: 427 YGLAAGIWTSDISKAHKTARAVRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHALEK 486 Query: 483 FTELKTIWISL 493 +TELK WI L Sbjct: 487 YTELKATWIKL 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: 659 Number of extensions: 18 Number of successful extensions: 2 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