GapMind for catabolism of small carbon sources

 

Aligments for a candidate for nbaE in Klebsiella michiganensis M5al

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate BWI76_RS10695 BWI76_RS10695 aldehyde dehydrogenase PuuC

Query= BRENDA::Q83XU8
         (485 letters)



>lcl|FitnessBrowser__Koxy:BWI76_RS10695 BWI76_RS10695 aldehyde
           dehydrogenase PuuC
          Length = 495

 Score =  335 bits (858), Expect = 3e-96
 Identities = 198/464 (42%), Positives = 271/464 (58%), Gaps = 15/464 (3%)

Query: 25  PLNNAVIAKVHEAGRAEVDAAVAAAQAAL-KGAWGRMSLAQRVEVLYAVADGINRRFDDF 83
           P     +A+V    +A+VD AV AA+    +G W + S AQR  VL   AD ++   ++ 
Sbjct: 42  PAAQQTLAEVARGKKADVDRAVQAARGVFDRGDWSQASPAQRKAVLTKFADLMDAHREEL 101

Query: 84  LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143
              E  DTGKP+  +   DIP  A   + +A+ +  V  E      P G   +   VR P
Sbjct: 102 ALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEV----APTGGNELAMIVREP 157

Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203
           +GV+  + PWN PLLL  WK+GPALA GN+VV+KPSE++P TA  L  +   AG+P GV+
Sbjct: 158 IGVIAAVVPWNFPLLLACWKLGPALASGNSVVLKPSEKSPLTALRLAGLAKQAGLPDGVF 217

Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADG-ARPVSLELGGKNAAIV 262
           NVV GFG +  G+ L  HPDV  ITFTG T T + ++K A D   + V LE GGK+A IV
Sbjct: 218 NVVSGFG-HEAGQALALHPDVEVITFTGSTRTAKQLLKDAGDSNMKRVWLEAGGKSANIV 276

Query: 263 FADC-DLDKAIEGTLRSCFANCGQVCLGTERVYVERPIFDRFVSRLKKGAEGMQLGRPED 321
           FADC DL KA+  T    F N GQVC+   R+ +E  I DRF+  LK+ A+G Q G P D
Sbjct: 277 FADCPDLQKAVNATAGGIFYNQGQVCIAGTRLLLEESIADRFLDLLKEQAKGWQPGNPLD 336

Query: 322 LATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGD 381
             T MG LI   H + V S+ + A EA +T++  G     P A      V PTI+  +  
Sbjct: 337 PNTTMGMLIDNTHADSVHSFIR-AGEAHSTLLLDGRKNPWPAA------VGPTIFVDVDP 389

Query: 382 DSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIA 441
            S +++EEIFGP  +V  F +EE+ +  AND+ YGL   +WT +LSRAHRV+  ++ G  
Sbjct: 390 ASPLSQEEIFGPVLVVTRFKNEEQALALANDSRYGLGAAVWTRDLSRAHRVSRRLKAGSV 449

Query: 442 WVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485
           +VN++   D+   FGG KQSG GR+  +H+LE +TELK + I L
Sbjct: 450 FVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWIAL 493


Lambda     K      H
   0.318    0.135    0.406 

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: 536
Number of extensions: 28
Number of successful extensions: 6
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: 485
Length of database: 495
Length adjustment: 34
Effective length of query: 451
Effective length of database: 461
Effective search space:   207911
Effective search space used:   207911
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.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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