GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Pseudomonas litoralis 2SM5

Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_090271605.1 BLU11_RS00885 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= BRENDA::Q9I6M4
         (426 letters)



>NCBI__GCF_900105005.1:WP_090271605.1
          Length = 417

 Score =  287 bits (734), Expect = 5e-82
 Identities = 153/396 (38%), Positives = 235/396 (59%), Gaps = 8/396 (2%)

Query: 22  QIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQV 81
           Q   V AER E   +   +G+ Y+DF  GI V +TGH HP V+AA +EQ+GKL H  +  
Sbjct: 10  QSSKVCAERGEGCWLIANDGKSYLDFTAGIGVTSTGHCHPTVVAAAREQVGKLIHAQYTT 69

Query: 82  LAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAATGRAGVIAFTGAYHG 141
           + ++P ++LAE +  ++P D         +GSEAVE A+++AR AT RA VI F G +HG
Sbjct: 70  VTHQPMLDLAERLVGKMP-DGIDSVAFSNAGSEAVEMALRLARHATRRANVIVFNGGFHG 128

Query: 142 RTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCEL-HGVSEDDS----IASIERIFKNDA 196
           RTM    +T            M  G+  A  P    +G SE+++    +A ++ I K   
Sbjct: 129 RTMGAASMTTSGTKVRNAYHPMMAGVVVAPFPHSWRYGWSEEEATRFCLAELDHILKTQT 188

Query: 197 QPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATE 256
            P+D AA++IEPVQGE G+Y  + +FMQ L   C QHGILL+ DE+Q G GR+G F++ +
Sbjct: 189 APEDTAAMVIEPVQGEFGYYPGNSAFMQGLAERCKQHGILLVCDEIQAGFGRSGKFWSHQ 248

Query: 257 QLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVF 316
             GI PD+   AK +  GFP+S +A    +M     G  GGTY  + ++CAAALA L+V 
Sbjct: 249 HFGITPDIVITAKGLASGFPLSAMAASQTLMAKGLAGSQGGTYGANAVSCAAALATLRVM 308

Query: 317 EEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSK 376
           + E L+  + A G++L   L+ ++ ++  + D+RG G M+ +E+ +  D  KP A+L + 
Sbjct: 309 DNENLVANAAARGQQLWDHLQILRQQYPQLADLRGKGLMLGLEIAQSPD--KPLADLAAS 366

Query: 377 IVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLE 412
           +   + E+GL+LL CGT   +IR+L P+ + +A+++
Sbjct: 367 LTTASEEEGLLLLRCGTDSQIIRWLPPLVVSEAEVD 402


Lambda     K      H
   0.319    0.137    0.393 

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: 402
Number of extensions: 15
Number of successful extensions: 4
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: 426
Length of database: 417
Length adjustment: 32
Effective length of query: 394
Effective length of database: 385
Effective search space:   151690
Effective search space used:   151690
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: 50 (23.9 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