Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_011842384.1 RSPH17029_RS17490 aldehyde dehydrogenase family protein
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_000015985.1:WP_011842384.1 Length = 791 Score = 293 bits (751), Expect = 1e-83 Identities = 175/469 (37%), Positives = 264/469 (56%), Gaps = 20/469 (4%) Query: 23 FINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAK 82 +I+G +T A E E +P T LA+I +I+ A++AAR F WS + Sbjct: 36 YIDGAFTGA-ETAAIEVENPATGEILARIPAAGEAEIEAAVAAARAAFS--GWSQLPGFE 92 Query: 83 RKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV 142 R L +A ++ ++LETLD GK IR + D+P A R +A V GE Sbjct: 93 RARYLYAIARGLQKRERFFSVLETLDNGKAIRETRTADVPLAIRHFYHHA-GWAAVLGEE 151 Query: 143 ATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIR 202 EP+GV ++PWNFP+L+ WK+ PALAAGN+V+LKP++ +PL+A+ Sbjct: 152 FPG---------HEPLGVCGQVIPWNFPMLMLAWKIAPALAAGNTVVLKPADLTPLTAVA 202 Query: 203 LAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMK 262 A + E GLP GV+N+V G G E G L RH + +AFTGST G+++ + S K Sbjct: 203 FAEMLDEIGLPRGVVNIVHG-GAETGALLVRHPGVAKVAFTGSTAVGREIRRATAGSG-K 260 Query: 263 RVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESIADEFLALL 322 + LE GGKS +V AD DL A G+++NQG+VC AG+RLLL+E IA+ FLA L Sbjct: 261 SLTLELGGKSPFVVCADA-DLDAAVEGVVEGVWFNQGEVCCAGSRLLLQEGIAERFLAKL 319 Query: 323 KQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGLAAA---I 379 + + + + G PLD +T MG ++ + I G ++ L+ L AA + Sbjct: 320 RARMEKIRVGDPLDKSTDMGAIVSARQKARIEELIA-GAAREGYRLEQAACPLPAAGHFV 378 Query: 380 GPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHR 439 P F D +P A++++ EIFGP+ V T F + ++A+ LAN++ YGL A+VW+ +++ A Sbjct: 379 APGFFADTEPAATVAQVEIFGPIAVTTTFRTVDEAVALANNTPYGLAASVWSENINAATE 438 Query: 440 MSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKT 488 ++ R++AG V++N N D FGG K+SG GR+ + L + +T Sbjct: 439 LAARIRAGVVWINASNLFDAGASFGGMKESGFGREGAREGLGAYLRPRT 487 Score = 89.7 bits (221), Expect = 3e-22 Identities = 66/212 (31%), Positives = 102/212 (48%), Gaps = 7/212 (3%) Query: 58 DIDRAMSAARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSL 117 DI A+ AA + W+ ++ R VL LA+ + A AE+LA L G R Sbjct: 555 DIRNAVEAA---LKAKGWAANAHG-RAQVLFFLAENIAARAEDLAA--ALVQGGAGRSEA 608 Query: 118 RDDIPGAARAIRWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWK 177 ++ + +YA DK G + T L + V+EP+GV+ + P PLL Sbjct: 609 AAEVRSLIERVFFYAGMADKDDGRIHATKPRHLTLSVKEPLGVVGVLAPDEAPLLSLMSL 668 Query: 178 LGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDI 237 + P +AAGN V+ PS L A L + + LP GV+N+VTG + + L+ H+ + Sbjct: 669 ILPLIAAGNRVVAVPSPAQALLAQPLTQIFDTSDLPGGVVNLVTGDRNLLARTLAEHDAV 728 Query: 238 DAIAFTGSTRTGKQLLKDAGDSNMKRVWLEAG 269 D I + GS + G ++ N+K+VW G Sbjct: 729 DGIWYHGSAK-GAAEVEALSAGNLKQVWTNGG 759 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: 943 Number of extensions: 54 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 495 Length of database: 791 Length adjustment: 37 Effective length of query: 458 Effective length of database: 754 Effective search space: 345332 Effective search space used: 345332 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: 54 (25.4 bits)
This GapMind analysis is from Apr 10 2024. 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