Alignments for a candidate for uxaA in Bacteroides thetaiotaomicron VPI-5482

GapMind for catabolism of small carbon sources

Alignments for a candidate for uxaA in Bacteroides thetaiotaomicron VPI-5482

Align Altronate dehydratase; D-altronate hydro-lyase; EC 4.2.1.7 (characterized)
to candidate 350014 BT0486 altronate hydrolase (NCBI ptt file)

Query= SwissProt::P42604
         (495 letters)



>FitnessBrowser__Btheta:350014
          Length = 496

 Score =  568 bits (1464), Expect = e-166
 Identities = 278/494 (56%), Positives = 359/494 (72%), Gaps = 1/494 (0%)

Query: 2   QYIKIHALDNVAVALADLAEGTEVSVDNQTVTLRQDVARGHKFALTDIAKGANVIKYGLP 61
           +Y++I+  DNVAVA+ +L  G  +SVD   +TL +D+  GHKFAL D A+G NVIKYG P
Sbjct: 4   KYLRINPADNVAVAIVNLPAGEHLSVDGIEITLNEDIPAGHKFALKDFAEGENVIKYGYP 63

Query: 62  IGYALADIAAGVHVHAHNTRTNLSDLDQYRYQPDFQDLPAQAADREVQIYRRANGDVGVR 121
           IG+A      G  ++  N +TNL+ L +Y Y P    L     +   + YRR NGDVGVR
Sbjct: 64  IGHARMAKKQGDWMNETNIKTNLAGLLEYTYHPTQVTLDIPHKNLTFKGYRRKNGDVGVR 123

Query: 122 NELWILPTVGCVNGIARQIQNRFLKETNNAEGTDGVFLFSHTYGCSQLGDDHINTRTMLQ 181
           NE+WI+PTVGCVNGI  Q+     +ET   +G D +  F H YGCSQLGDDH NT+ +L+
Sbjct: 124 NEIWIIPTVGCVNGIIGQLAEGLRRETEG-KGVDAIVAFPHNYGCSQLGDDHENTKKILR 182

Query: 182 NMVRHPNAGAVLVIGLGCENNQVAAFRETLGDIDPERVHFMICQQQDDEIEAGIEHLHQL 241
           +MV HPNAGAVL++GLGCENNQ   FRE LGD D +RV FM+ Q+  DE E G++ L  L
Sbjct: 183 DMVLHPNAGAVLIVGLGCENNQPDVFREFLGDYDQDRVKFMVTQKVGDEYEEGMDILRDL 242

Query: 242 YNVMRNDKREPGKLSELKFGLECGGSDGLSGITANPMLGRFSDYVIANGGTTVLTEVPEM 301
           Y     D+R    LSEL+ GL+CGGSDG SGITANP+LG FSD++IA GGT+VLTEVPEM
Sbjct: 243 YAKASKDERTEVPLSELRVGLKCGGSDGFSGITANPLLGMFSDFLIAQGGTSVLTEVPEM 302

Query: 302 FGAEQLLMDHCRDEATFEKLVTMVNDFKQYFIAHDQPIYENPSPGNKAGGITTLEDKSLG 361
           FGAE +LM+ C ++  FE+ V ++NDFK+YF++H +P+ ENPSPGNKAGGI+TLE+K+LG
Sbjct: 303 FGAETILMNRCENKDLFEQTVHLINDFKEYFLSHGEPVGENPSPGNKAGGISTLEEKALG 362

Query: 362 CTQKAGSSVVVDVLRYGERLKTPGLNLLSAPGNDAVATSALAGAGCHMVLFSTGRGTPYG 421
           CTQK G S V  V+ YGERL+  GLNLLSAPGND VA + LA +GCHMVLF+TGRGTP+G
Sbjct: 363 CTQKCGKSYVSGVMPYGERLQKKGLNLLSAPGNDLVAATTLAASGCHMVLFTTGRGTPFG 422

Query: 422 GFVPTVKIATNSELAAKKKHWIDFDAGQLIHGKAMPQLLEEFIDTIVEFANGKQTCNERN 481
            FVPT+KI+TNS LA  K  WIDF+AG ++  + M +  E FI+ +++ A+G+   NE+ 
Sbjct: 423 TFVPTMKISTNSTLAKNKPGWIDFNAGVIVENEPMEKTCERFIEYVIKVASGEFVNNEKK 482

Query: 482 DFRELAIFKSGVTL 495
            +RE+AIFK+GVTL
Sbjct: 483 GYREIAIFKTGVTL 496


Lambda     K      H
   0.319    0.136    0.403 

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: 753
Number of extensions: 32
Number of successful extensions: 2
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: 496
Length adjustment: 34
Effective length of query: 461
Effective length of database: 462
Effective search space:   212982
Effective search space used:   212982
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources