GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysN in Pseudomonas litoralis 2SM5

Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_090271605.1 BLU11_RS00885 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme

Query= reanno::Putida:PP_4108
         (416 letters)



>NCBI__GCF_900105005.1:WP_090271605.1
          Length = 417

 Score =  239 bits (610), Expect = 1e-67
 Identities = 142/391 (36%), Positives = 206/391 (52%), Gaps = 8/391 (2%)

Query: 30  DGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLALMEQLSQFVP 89
           DGK Y+DF  GIGV + GHC+P VV A + Q  +L H  +    H P L L E+L   +P
Sbjct: 28  DGKSYLDFTAGIGVTSTGHCHPTVVAAAREQVGKLIHAQYTTVTHQPMLDLAERLVGKMP 87

Query: 90  VSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRTLATLNLNGKVAPYKQR 149
                    +N+G+EA E AL++AR AT +  +I F+GGFHGRT+   ++       +  
Sbjct: 88  DGIDSVAF-SNAGSEAVEMALRLARHATRRANVIVFNGGFHGRTMGAASMTTSGTKVRNA 146

Query: 150 VGELPGPVYHLPYP-SADTGVTCEQA----LKAMDRLFSVELAVEDVAAFIFEPVQGEGG 204
              +   V   P+P S   G + E+A    L  +D +   + A ED AA + EPVQGE G
Sbjct: 147 YHPMMAGVVVAPFPHSWRYGWSEEEATRFCLAELDHILKTQTAPEDTAAMVIEPVQGEFG 206

Query: 205 FLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDLLLLAKSIAGG 264
           +   + AF Q L   C + GIL++ DEIQ+GFGR+G+ ++    GI PD+++ AK +A G
Sbjct: 207 YYPGNSAFMQGLAERCKQHGILLVCDEIQAGFGRSGKFWSHQHFGITPDIVITAKGLASG 266

Query: 265 MPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQMTDENLATWGERQEQAIVS 324
            PL A+   + LMA    G  GGTY  N +SCAAALA+L  M +ENL      + Q +  
Sbjct: 267 FPLSAMAASQTLMAKGLAGSQGGTYGANAVSCAAALATLRVMDNENLVANAAARGQQLWD 326

Query: 325 RYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEAARARGLLLMPSGKA 384
             +  +     P +  L G G M G+E A +   P     A +  A+   GLLL+  G  
Sbjct: 327 HLQILRQQ--YPQLADLRGKGLMLGLEIAQSPDKPLADLAASLTTASEEEGLLLLRCGTD 384

Query: 385 RHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
             IIR L PL +    +++ +    + LA +
Sbjct: 385 SQIIRWLPPLVVSEAEVDDAVQRFTRVLARV 415


Lambda     K      H
   0.320    0.137    0.402 

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: 408
Number of extensions: 28
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: 416
Length of database: 417
Length adjustment: 31
Effective length of query: 385
Effective length of database: 386
Effective search space:   148610
Effective search space used:   148610
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