GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nbaE in Escherichia coli BW25113

Align aminomuconate-semialdehyde dehydrogenase (EC 1.2.1.32) (characterized)
to candidate 15420 b1300 gamma-Glu-gamma-aminobutyraldehyde dehydrogenase, NAD(P)H-dependent (NCBI)

Query= BRENDA::Q83XU8
         (485 letters)



>FitnessBrowser__Keio:15420
          Length = 495

 Score =  320 bits (821), Expect = 5e-92
 Identities = 185/464 (39%), Positives = 269/464 (57%), Gaps = 15/464 (3%)

Query: 25  PLNNAVIAKVHEAGRAEVDAAVAAAQAAL-KGAWGRMSLAQRVEVLYAVADGINRRFDDF 83
           P+  A +AK+      ++D A++AA+    +G W   S A+R  VL  +AD +    ++ 
Sbjct: 42  PVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSPAKRKAVLNKLADLMEAHAEEL 101

Query: 84  LAAEVEDTGKPMSLARHVDIPRGAANFKIFADVVKNVPTEFFEMPTPDGVGAINYAVRRP 143
              E  DTGKP+  +   DIP  A   + +A+ +  V  E     + +    +   VR P
Sbjct: 102 ALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGEVATTSSHE----LAMIVREP 157

Query: 144 VGVVGVICPWNLPLLLMTWKVGPALACGNTVVVKPSEETPQTAALLGEVMNTAGVPPGVY 203
           VGV+  I PWN PLLL  WK+GPALA GN+V++KPSE++P +A  L  +   AG+P GV 
Sbjct: 158 VGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSEKSPLSAIRLAGLAKEAGLPDGVL 217

Query: 204 NVVHGFGPNSTGEFLTSHPDVNAITFTGETGTGEAIMKAAADG-ARPVSLELGGKNAAIV 262
           NVV GFG +  G+ L+ H D++AI FTG T TG+ ++K A D   + V LE GGK+A IV
Sbjct: 218 NVVTGFG-HEAGQALSRHNDIDAIAFTGSTRTGKQLLKDAGDSNMKRVWLEAGGKSANIV 276

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

Query: 322 LATGMGPLISQEHREKVLSYYKKAVEAGATVVTGGGVPEMPEALKGGAWVQPTIWTGLGD 381
            AT MG LI   H + V S+ ++    G  ++ G             A + PTI+  +  
Sbjct: 337 PATTMGTLIDCAHADSVHSFIREGESKGQLLLDGRNAGL-------AAAIGPTIFVDVDP 389

Query: 382 DSVVAREEIFGPCALVMPFDSEEEVIRRANDNDYGLARRIWTTNLSRAHRVAGAIEVGIA 441
           ++ ++REEIFGP  +V  F SEE+ ++ AND+ YGL   +WT +LSRAHR++  ++ G  
Sbjct: 390 NASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRDLSRAHRMSRRLKAGSV 449

Query: 442 WVNSWFLRDLRTAFGGSKQSGIGREGGVHSLEFYTELKNVCIKL 485
           +VN++   D+   FGG KQSG GR+  +H+LE +TELK + I L
Sbjct: 450 FVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISL 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: 527
Number of extensions: 32
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 (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:

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. 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