Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate WP_090442712.1 BLS63_RS08515 aldehyde dehydrogenase
Query= BRENDA::P23883 (495 letters) >NCBI__GCF_900100495.1:WP_090442712.1 Length = 497 Score = 500 bits (1288), Expect = e-146 Identities = 254/489 (51%), Positives = 332/489 (67%), Gaps = 4/489 (0%) Query: 9 WQDKALSLAIENRLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARG 68 WQ +A ++ I+G+ A TF +++P LA++A + D+D A+++AR Sbjct: 7 WQRRAAEQGFISQALIDGQLRPAQSGATFASINPANNQLLAEVAACDAADVDAAVASARQ 66 Query: 69 VFERGDWSLSSPAKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAI 128 FE+G W+ +P +RK VL +LA+L+ A+ EELALL++L+ GKP+ + D+PGAA Sbjct: 67 AFEQGPWARMAPRERKQVLLRLAELIMANREELALLDSLNMGKPVMDAYTIDVPGAANVF 126 Query: 129 RWYAEAIDKVYGEVATTSSHELAMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSV 188 WYAEA+DK Y ++A T+S LA I REP+GVI A+VPWNFPL L WKL PALAAGNSV Sbjct: 127 AWYAEALDKRYDQIAPTASDALATISREPLGVIGAVVPWNFPLDLAAWKLSPALAAGNSV 186 Query: 189 ILKPSEKSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRT 248 +LKP+E+SP SA+RL LA EAGLP GVLNV+ G G AG+AL H D+D +AFTGST Sbjct: 187 VLKPAEQSPFSALRLGQLALEAGLPAGVLNVLPGLGESAGKALGLHMDVDCLAFTGSTEV 246 Query: 249 GKQLLKDAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRL 308 GK + A SN+K+VWLE GGKSAN+VFADC DL AA A IF+NQG+VC A +RL Sbjct: 247 GKCFMAYAAQSNLKQVWLECGGKSANLVFADCQDLDLAAEKAAFAIFFNQGEVCSANSRL 306 Query: 309 LLEESIADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREGESKGQLLL 368 L+E + DEF+ L +A+ WQPG PL+PA+ G ++D A+ + FI + +G L+ Sbjct: 307 LVERRVHDEFVQRLIAKAREWQPGDPLNPASRAGAIVDSRQAERIMGFIDRAQGQGATLV 366 Query: 369 DGRN----AGLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYG 424 G G I PT F V P L+REE+FGPVL V F SEEQA+ LANDS YG Sbjct: 367 CGGQRLSVGGSDNFIQPTTFTGVSPAMQLAREEVFGPVLAVLPFDSEEQAIALANDSLYG 426 Query: 425 LGAAVWTRDLSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFT 484 L A++WT DL+RAHR++RRL+AGSV VN + D+ VPFGG KQSG GRD SLHA +K++ Sbjct: 427 LAASLWTDDLNRAHRVARRLRAGSVSVNTVDALDVCVPFGGCKQSGFGRDLSLHAFDKYS 486 Query: 485 ELKTIWISL 493 LKT W L Sbjct: 487 LLKTTWFQL 495 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: 610 Number of extensions: 22 Number of successful extensions: 3 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 24 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