Align 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase (NADP+) (EC 1.2.1.77) (characterized)
to candidate GFF2643 PGA1_c26830 phenylacetic acid degradation protein PaaZ
Query= BRENDA::Q13WK4 (531 letters) >FitnessBrowser__Phaeo:GFF2643 Length = 676 Score = 418 bits (1075), Expect = e-121 Identities = 228/513 (44%), Positives = 313/513 (61%), Gaps = 11/513 (2%) Query: 5 LKNHVAGQWIAGTGAGITLTDPVTGVALVRVSSEGLDLARAFSFAREDGGAALRALTYAQ 64 + + AGQWIA ++ +TG L + ++ LD+ +AR GG +LR LT+ Sbjct: 6 VSSFAAGQWIAPGAGARSIASAITGAPLAQAGNDALDVQGMLDYARTVGGPSLRKLTFHD 65 Query: 65 RAARLADIVKLLQAKRGDYYAIATANSGTTRNDSAVDIDGGIFTLSYYAKLGA-SLGEVH 123 RA L + L + Y ++ N+G T++D +DIDGGI T+ +A G + + H Sbjct: 66 RARMLKALAGHLNQHKQALYDLSF-NTGATQSDHMIDIDGGIGTMFVFASKGRREMPDAH 124 Query: 124 ALRDGSAESLSKDRSFSAQHVLSPTRGVALFINAFNFPSWGLWEKAAPALLSGVPVIVKP 183 DG E LS++ +F QH+ +P +GVA+ INAFNFP WG+ EK AP LL+GVP IVKP Sbjct: 125 VYLDGDIEQLSRNGTFLGQHICTPLQGVAVHINAFNFPVWGMLEKLAPTLLAGVPAIVKP 184 Query: 184 ATATAWLTQRMVADVVDAGILPPGALSIICGSSAGLLDQIRSFDVVSFTGSADTAATLRA 243 ATAT ++T+ V ++++GILP GAL ++ G +LD + DVVSFTGSA TA LRA Sbjct: 185 ATATCYVTELAVRLMLESGILPEGALQLVSGGLGDMLDHLTMQDVVSFTGSAQTALKLRA 244 Query: 244 HPAFVQRGARLNVEADSLNSAILCADATPDTPAFDLFIKEVVREMTVKSGQKCTAIRRAF 303 +P ++ R E DSLN++IL DA P TP FDLF+KEV REMT K+GQKCTAIRR Sbjct: 245 NPVILENSIRFVAEQDSLNASILGPDAGPGTPEFDLFVKEVSREMTTKAGQKCTAIRRII 304 Query: 304 VPEAALEPVLEALKAKLAKITVGNPRNDAVRMGSLVSREQYENVLAGIAALREEAVLAY- 362 P+A +E V+EAL A+LAK +G+PR + RMG+LVS Q +VL A + +EA + Sbjct: 305 APDAQVEAVIEALSARLAKTRIGDPRLETTRMGALVSNSQKRDVLEKAAIIGQEAERVFG 364 Query: 363 DSSAVPLIDADANIAACVAPHLFVVNDPDNATLLHDVEVFGPVASVAPYRVTTDTNALPE 422 D + ADA A V P LF DPD A +HD E FGPV+++ Y Sbjct: 365 DPENFSVDGADAEKGAFVPPMLFHCADPDKAQRVHDTEAFGPVSTIMGYHDLD------- 417 Query: 423 AHAVALARRGQGSLVASIYSNDDAHLGRLALELADSHGRVHAISPSVQHSQTGHGNVMPM 482 HA+ LA RG+GSLVAS+ ++D +AL HGR++ + TGHG+ +P Sbjct: 418 -HAITLANRGEGSLVASVITHDTEVAREVALGAGAYHGRLYFNNRDSMKESTGHGSPLPH 476 Query: 483 SLHGGPGRAGGGEELGGLRALAFYHRRSAIQAA 515 +HGGPGRAGGGEELGG+R + Y +R+AIQ + Sbjct: 477 MVHGGPGRAGGGEELGGVRGVKHYMQRTAIQGS 509 Lambda K H 0.318 0.132 0.379 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: 805 Number of extensions: 34 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: 531 Length of database: 676 Length adjustment: 37 Effective length of query: 494 Effective length of database: 639 Effective search space: 315666 Effective search space used: 315666 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: 53 (25.0 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