GapMind for catabolism of small carbon sources

 

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

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate 354228 BT4702 dihydroxynapthoic acid synthetase (NCBI ptt file)

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__Btheta:354228
          Length = 274

 Score =  130 bits (327), Expect = 3e-35
 Identities = 90/264 (34%), Positives = 136/264 (51%), Gaps = 15/264 (5%)

Query: 2   EFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KA 60
           E+E I       +  IT+NR    NA       E+  A+     + +I VI+ITG G KA
Sbjct: 12  EYEDILFDYYNGIARITINRERYRNAFTPTTTAEMSDALRICREEADIDVIVITGAGDKA 71

Query: 61  FCAGADITQFNQLTPAEAWKFSKKG------REIMDKIEALSKPTIAMINGYALGGGLEL 114
           FC+G D     Q          K G       ++  +I ++ KP IA +NG+A+GGG  L
Sbjct: 72  FCSGGD-----QNVKGRGGYIGKDGVPRLSVLDVQKQIRSIPKPVIAAVNGFAIGGGHVL 126

Query: 115 ALACDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEK 174
            + CD+ IA+E A  G     +G +    G   L RV+G+ +A E+     +   ++A  
Sbjct: 127 HVVCDLSIASENAIFGQTGPRVGSFDAGFGASYLARVVGQKKAREIWFLCRKYNAQEALD 186

Query: 175 YGLVNRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGL-ALESVGWG 233
            GLVN+VVPL  LE E  + AE++   SP++L +IK  +N  LD    +G+  L      
Sbjct: 187 MGLVNKVVPLEQLEDEYVQWAEEMMLLSPLALRMIKAGLNAELDGQ--AGIQELAGDATL 244

Query: 234 VVFSTEDKKEGVSAFLEKREPTFK 257
           + + T++ +EG +AFLEKR+P FK
Sbjct: 245 LYYLTDEAQEGKNAFLEKRKPNFK 268


Lambda     K      H
   0.315    0.135    0.382 

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: 148
Number of extensions: 9
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: 259
Length of database: 274
Length adjustment: 25
Effective length of query: 234
Effective length of database: 249
Effective search space:    58266
Effective search space used:    58266
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: 42 (22.0 bits)
S2: 47 (22.7 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