GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Klebsiella michiganensis M5al

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate BWI76_RS13115 BWI76_RS13115 2,3-dehydroadipyl-CoA hydratase

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__Koxy:BWI76_RS13115
          Length = 255

 Score =  177 bits (449), Expect = 2e-49
 Identities = 101/252 (40%), Positives = 148/252 (58%), Gaps = 6/252 (2%)

Query: 10  KEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQ 69
           +   +  +TLNRP   NALN  LL ++   +  A  DP + V +I+G  + F AGAD+ +
Sbjct: 8   RHARVLQLTLNRPQARNALNNALLMQIADVLDAAALDPTVGVCVISGNERFFAAGADLNE 67

Query: 70  F--NQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEA 127
              N L PA       +   +  +I+A SKP IA +NGYALG G ELAL CD+ +A + A
Sbjct: 68  MAENDL-PATLDDIRPR---LWARIDAFSKPLIASVNGYALGAGCELALICDLIVAGDNA 123

Query: 128 QLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANL 187
           + GLPEI LG+ PG GGTQRL R +GK  A  M+++G+ I    A + GLV+ V P A  
Sbjct: 124 RFGLPEITLGMMPGAGGTQRLIRSVGKALASRMVLSGESIDAHQALRAGLVSEVYPPALT 183

Query: 188 EQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSA 247
           ++    LA  +A+ SP++L   K+ +    +  L +GL  E   + ++ +TED++EG+ A
Sbjct: 184 DEYALSLAATVARHSPLALRAAKQSLRLSQEVSLQAGLQQERQLFTLLSATEDRREGIDA 243

Query: 248 FLEKREPTFKGK 259
           FL KR   FKG+
Sbjct: 244 FLHKRTAEFKGR 255


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: 114
Number of extensions: 7
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: 259
Length of database: 255
Length adjustment: 24
Effective length of query: 235
Effective length of database: 231
Effective search space:    54285
Effective search space used:    54285
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