GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaG in Klebsiella michiganensis M5al

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate BWI76_RS13115 BWI76_RS13115 2,3-dehydroadipyl-CoA hydratase

Query= BRENDA::P77467
         (262 letters)



>FitnessBrowser__Koxy:BWI76_RS13115
          Length = 255

 Score =  133 bits (335), Expect = 3e-36
 Identities = 87/259 (33%), Positives = 132/259 (50%), Gaps = 8/259 (3%)

Query: 4   FILSHVEKGVMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCAG 63
           FI  H    V+ LTLNRP+  N+ N+ +  Q+A+ L     D T+   +++G  R F AG
Sbjct: 5   FIARHAR--VLQLTLNRPQARNALNNALLMQIADVLDAAALDPTVGVCVISGNERFFAAG 62

Query: 64  QDLNDRNVDPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDI 123
            DLN+   +      DL  +++     L  R+    KP+I +VNG A GAG  LAL  D+
Sbjct: 63  ADLNEMAEN------DLPATLDDIRPRLWARIDAFSKPLIASVNGYALGAGCELALICDL 116

Query: 124 VIAARSAKFVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQ 183
           ++A  +A+F +    LG++P  GGT  L R  G+A A  + L G  + A QA   G++ +
Sbjct: 117 IVAGDNARFGLPEITLGMMPGAGGTQRLIRSVGKALASRMVLSGESIDAHQALRAGLVSE 176

Query: 184 VVDDETLADTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSAD 243
           V       + A  LA  +A      L   KQ++  ++  +L   L  ER    L   + D
Sbjct: 177 VYPPALTDEYALSLAATVARHSPLALRAAKQSLRLSQEVSLQAGLQQERQLFTLLSATED 236

Query: 244 YREGVSAFLAKRSPQFTGK 262
            REG+ AFL KR+ +F G+
Sbjct: 237 RREGIDAFLHKRTAEFKGR 255


Lambda     K      H
   0.321    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: 110
Number of extensions: 5
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: 262
Length of database: 255
Length adjustment: 24
Effective length of query: 238
Effective length of database: 231
Effective search space:    54978
Effective search space used:    54978
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 (21.8 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