GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gloA in Paraburkholderia bryophila 376MFSha3.1

Align Protein DJ-1 homolog D; AtDJ1D; Lactoylglutathione lyase DJ1D; EC 4.4.1.5 (characterized)
to candidate H281DRAFT_05074 H281DRAFT_05074 protease I

Query= SwissProt::Q9M8R4
         (388 letters)



>FitnessBrowser__Burk376:H281DRAFT_05074
          Length = 193

 Score =  233 bits (595), Expect = 3e-66
 Identities = 111/191 (58%), Positives = 140/191 (73%), Gaps = 1/191 (0%)

Query: 196 ANKRILFLCGDYMEDYEVKVPFQSLQALGCQVDAVCPEKKAGDRCPTAIHDFEGDQTYSE 255
           A K+ILFL GD+ EDYE  VPFQ+LQA+G  VDAVCP+KKAGDR  TAIHDFEGDQTY+E
Sbjct: 2   AAKKILFLTGDFAEDYETMVPFQALQAVGHVVDAVCPDKKAGDRIKTAIHDFEGDQTYTE 61

Query: 256 KPGHTFALTTNFDDLVSSSYDALVIPGGRAPEYLALNEHVLNIVKEFMNSEKPVASICHG 315
           KPGH FAL  +F+D     YDAL I GGRAPEYL LN  V+ +V++F  + KP+A+ICH 
Sbjct: 62  KPGHLFALNASFEDADPRQYDALAIAGGRAPEYLRLNPKVIELVRQFAEAGKPIAAICHA 121

Query: 316 QQILAAAGVLKGRKCTAYPAVKLNVVLGGGTWLEPDPIDRCFTDGNLVTGAAWPGHPEFV 375
            Q+LAAA V++G++ +AYPA    V L GG + +  P+D   TDGN VT  AWP HPE++
Sbjct: 122 AQLLAAADVIRGKRISAYPACAPEVKLAGGEFAD-IPVDAAITDGNFVTAPAWPAHPEWL 180

Query: 376 SQLMALLGIQV 386
            Q + LLG ++
Sbjct: 181 RQFLVLLGTRI 191



 Score =  199 bits (507), Expect = 4e-56
 Identities = 95/190 (50%), Positives = 128/190 (67%), Gaps = 1/190 (0%)

Query: 4   SRTVLILCGDYMEDYEVMVPFQALQAFGITVHTVCPGKKAGDSCPTAVHDFCGHQTYFES 63
           ++ +L L GD+ EDYE MVPFQALQA G  V  VCP KKAGD   TA+HDF G QTY E 
Sbjct: 3   AKKILFLTGDFAEDYETMVPFQALQAVGHVVDAVCPDKKAGDRIKTAIHDFEGDQTYTEK 62

Query: 64  RGHNFTLNATFDEVDLSKYDGLVIPGGRAPEYLALTASVVELVKEFSRSGKPIASICHGQ 123
            GH F LNA+F++ D  +YD L I GGRAPEYL L   V+ELV++F+ +GKPIA+ICH  
Sbjct: 63  PGHLFALNASFEDADPRQYDALAIAGGRAPEYLRLNPKVIELVRQFAEAGKPIAAICHAA 122

Query: 124 LILAAADTVNGRKCTAYATVGPSLVAAGAKWVEPITPDVCVVDGSLITAATYEGHPEFIQ 183
            +LAAAD + G++ +AY    P +  AG ++ + I  D  + DG+ +TA  +  HPE+++
Sbjct: 123 QLLAAADVIRGKRISAYPACAPEVKLAGGEFAD-IPVDAAITDGNFVTAPAWPAHPEWLR 181

Query: 184 LFVKALGGKI 193
            F+  LG +I
Sbjct: 182 QFLVLLGTRI 191


Lambda     K      H
   0.321    0.138    0.425 

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: 305
Number of extensions: 7
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 388
Length of database: 193
Length adjustment: 25
Effective length of query: 363
Effective length of database: 168
Effective search space:    60984
Effective search space used:    60984
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)

Align Protein DJ-1 homolog D; AtDJ1D; Lactoylglutathione lyase DJ1D; EC 4.4.1.5 (characterized)
to candidate H281DRAFT_00047 H281DRAFT_00047 protease I

Query= SwissProt::Q9M8R4
         (388 letters)



>FitnessBrowser__Burk376:H281DRAFT_00047
          Length = 193

 Score =  211 bits (538), Expect = 1e-59
 Identities = 101/191 (52%), Positives = 137/191 (71%), Gaps = 1/191 (0%)

Query: 196 ANKRILFLCGDYMEDYEVKVPFQSLQALGCQVDAVCPEKKAGDRCPTAIHDFEGDQTYSE 255
           A KRI+FL GD+ EDYE+ VPFQ+L+ +G +VD VCP KK GD+  TAIHDFEGDQTY+E
Sbjct: 2   AAKRIVFLTGDFAEDYEMMVPFQALEMIGHKVDTVCPGKKRGDKIKTAIHDFEGDQTYTE 61

Query: 256 KPGHTFALTTNFDDLVSSSYDALVIPGGRAPEYLALNEHVLNIVKEFMNSEKPVASICHG 315
           KPGH F L  NFDD+    YDAL+I GGRAPEYL LNE V+ IV+EF  + K +A++CHG
Sbjct: 62  KPGHLFILNANFDDVEVDDYDALMIVGGRAPEYLRLNERVVEIVQEFAGAGKLIAAVCHG 121

Query: 316 QQILAAAGVLKGRKCTAYPAVKLNVVLGGGTWLEPDPIDRCFTDGNLVTGAAWPGHPEFV 375
            Q+LAAA V++G++ + YPA   ++ L GG + +   +D   TDGN VT   +  HP ++
Sbjct: 122 AQLLAAADVIRGKRISGYPACAPDIRLAGGEYAD-IRMDDAITDGNFVTCPVYLAHPRWL 180

Query: 376 SQLMALLGIQV 386
           +Q++  LG ++
Sbjct: 181 AQVLLQLGTEI 191



 Score =  189 bits (481), Expect = 4e-53
 Identities = 91/190 (47%), Positives = 125/190 (65%), Gaps = 1/190 (0%)

Query: 4   SRTVLILCGDYMEDYEVMVPFQALQAFGITVHTVCPGKKAGDSCPTAVHDFCGHQTYFES 63
           ++ ++ L GD+ EDYE+MVPFQAL+  G  V TVCPGKK GD   TA+HDF G QTY E 
Sbjct: 3   AKRIVFLTGDFAEDYEMMVPFQALEMIGHKVDTVCPGKKRGDKIKTAIHDFEGDQTYTEK 62

Query: 64  RGHNFTLNATFDEVDLSKYDGLVIPGGRAPEYLALTASVVELVKEFSRSGKPIASICHGQ 123
            GH F LNA FD+V++  YD L+I GGRAPEYL L   VVE+V+EF+ +GK IA++CHG 
Sbjct: 63  PGHLFILNANFDDVEVDDYDALMIVGGRAPEYLRLNERVVEIVQEFAGAGKLIAAVCHGA 122

Query: 124 LILAAADTVNGRKCTAYATVGPSLVAAGAKWVEPITPDVCVVDGSLITAATYEGHPEFIQ 183
            +LAAAD + G++ + Y    P +  AG ++ + I  D  + DG+ +T   Y  HP ++ 
Sbjct: 123 QLLAAADVIRGKRISGYPACAPDIRLAGGEYAD-IRMDDAITDGNFVTCPVYLAHPRWLA 181

Query: 184 LFVKALGGKI 193
             +  LG +I
Sbjct: 182 QVLLQLGTEI 191


Lambda     K      H
   0.321    0.138    0.425 

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: 317
Number of extensions: 9
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 388
Length of database: 193
Length adjustment: 25
Effective length of query: 363
Effective length of database: 168
Effective search space:    60984
Effective search space used:    60984
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 Apr 09 2024. 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