Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate SMa0796 SMa0796 hypothetical protein
Query= BRENDA::P23883 (495 letters) >FitnessBrowser__Smeli:SMa0796 Length = 487 Score = 338 bits (867), Expect = 3e-97 Identities = 200/474 (42%), Positives = 286/474 (60%), Gaps = 12/474 (2%) Query: 23 FINGEYTAAAENET-FETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPA 81 +INGE+ A+ E FE++DP T A++ + D++RA+ AAR WS + Sbjct: 7 YINGEF---ADGEARFESIDPTTGRAWAEMPEAREADVNRAVEAARIALHDQPWSTLTAT 63 Query: 82 KRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGE 141 +R +L KLADL+ +A LA LET DTGK IR + I A R+YA DK+ G Sbjct: 64 QRGKLLYKLADLVAENAGRLAELETRDTGKIIRET-SSQIAYVADYYRYYAGIADKIEGS 122 Query: 142 VATTSSHELAM-IVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSA 200 ++ + + REP+GV+A +VPWN L L+ K+GPALAAG ++++K SE P Sbjct: 123 YLPIDKPDMDVWLRREPIGVVAMVVPWNSQLFLSAVKIGPALAAGCTMVVKASEDGPAPL 182 Query: 201 IRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSN 260 + A L AG P GV+N+VTGFG G ALSRH +D IAFTG T + +++++ + N Sbjct: 183 LEFARLVHAAGFPAGVVNIVTGFGPSCGAALSRHPQVDHIAFTGGPETARHIVRNSAE-N 241 Query: 261 MKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLA 320 + LE GGKS IVFAD DL+ AA+A AGIF GQ C+AG+RL++E+S+ D FL Sbjct: 242 LASTSLELGGKSPFIVFADA-DLESAANAQIAGIFAATGQSCVAGSRLIVEKSVKDRFLQ 300 Query: 321 LLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNA--GLAAA 378 +LK +A+ + G PL+ +T +G L ++ V + + + G L+ G A G Sbjct: 301 ILKAKAETIRIGSPLEMSTEVGPLATERQSNHVKTLVARSLAAGAKLVTGGTAPEGAGFY 360 Query: 379 IGPTIFVDVDPNASLSRE-EIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRA 437 PTI +D D +AS S E E FGPVL V F +E +AL LANDS++GL A V+T++L+RA Sbjct: 361 YRPTI-LDCDGSASPSLENEFFGPVLSVLSFETEAEALHLANDSRFGLAAGVFTQNLTRA 419 Query: 438 HRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491 HR+ + ++AG V+VN Y PFGG+ SG+GR+ L A +T KT+W+ Sbjct: 420 HRLMKGIRAGIVWVNTYRAVSPVAPFGGFGLSGHGREGGLEAALDYTRSKTVWL 473 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: 551 Number of extensions: 24 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: 487 Length adjustment: 34 Effective length of query: 461 Effective length of database: 453 Effective search space: 208833 Effective search space used: 208833 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