GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Erythrobacter marinus HWDM-33

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate WP_047094365.1 AAV99_RS12275 enoyl-CoA hydratase/isomerase family protein

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>NCBI__GCF_001013305.1:WP_047094365.1
          Length = 252

 Score = 94.0 bits (232), Expect = 3e-24
 Identities = 80/262 (30%), Positives = 118/262 (45%), Gaps = 24/262 (9%)

Query: 5   NILVETRGRVGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGSEKA--FA 62
           N+ +E  G V  + ++R    NA N A+ + +   L +  AD A+  +V+  ++    F 
Sbjct: 2   NLRLEFDGPVAHLLIDRLDKRNAFNMAMWEAMPGLLEQARADPAVRTLVIRSAQPGGVFC 61

Query: 63  AGADIGMMSTYTYMDVYKGDYITRNWETVRSIRK-------PIIAAVAGFALGGGCELAM 115
           AGADI  M  +       G ++  N   +  ++        P +A V G  +GGGC +A+
Sbjct: 62  AGADIKEMLLHKD----DGAWLAANQAAINRVQHDLARLTLPTVAFVEGDCVGGGCGIAI 117

Query: 116 MCDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAERAG 175
            CD+  A D A+FG    KLGI+      + L   V   +A  +  T   +DAAEA+R G
Sbjct: 118 ACDLRVATDKARFGITPGKLGIVYPLHDVKLLTDLVGPGQAKRMLFTGGLLDAAEAQRIG 177

Query: 176 LVSRVI--PAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHS 233
           LV  +   P   L D   A+  +I E     V  V +      + TLA        +F  
Sbjct: 178 LVEMIADSPRGLLNDILSASPHSIREI-KMFVRRVLDGQTGDDDQTLA--------IFTD 228

Query: 234 LFATEDQKEGMAAFVEKRKPVF 255
            F   D  EG AAF  KRKP F
Sbjct: 229 AFMRGDFAEGAAAFAGKRKPDF 250


Lambda     K      H
   0.321    0.134    0.380 

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: 137
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: 258
Length of database: 252
Length adjustment: 24
Effective length of query: 234
Effective length of database: 228
Effective search space:    53352
Effective search space used:    53352
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 (21.9 bits)
S2: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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