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_090273343.1 BLU11_RS10765 aspartate aminotransferase family protein

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



>NCBI__GCF_900105005.1:WP_090273343.1
          Length = 404

 Score =  192 bits (488), Expect = 2e-53
 Identities = 139/402 (34%), Positives = 196/402 (48%), Gaps = 36/402 (8%)

Query: 21  GRNAEVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLTHYAFNAAPHGPYLAL 80
           G  + +WD  G+ YID  GGI V +LGH +P +VEA+  QA +L H + N   + P L L
Sbjct: 30  GDGSRLWDQQGREYIDLAGGIAVNSLGHAHPQLVEALTEQAQKLWHVS-NIMTNEPALRL 88

Query: 81  MEQLSQFVPVSYPLAGMLTNSGAEAAENALKVAR------GATGKRAIIAFDGGFHGRTL 134
            ++L   V  ++    +  NSGAEA E A K+AR          K  IIA    FHGRTL
Sbjct: 89  ADKL---VAATFADKVLFVNSGAEANEAAFKLARRWAHDQSGPDKHEIIACSNSFHGRTL 145

Query: 135 ATLNLNGKVAPYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVAAF 194
            T+++ G+   Y Q  G     + H+PY            + A++   S     E   A 
Sbjct: 146 FTVSVGGQ-PKYSQGFGPAISGISHVPYND----------IAALEAQIS-----ERTCAV 189

Query: 195 IFEPVQGEGGFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDL 254
           + EPVQGEGG +     + +A+R  CD+   L+I DE+QSG GRTG+ +A+   G+ PD+
Sbjct: 190 VVEPVQGEGGVIPASIEYLKAVRALCDKYNALLIFDEVQSGMGRTGKLYAYMHSGVAPDI 249

Query: 255 LLLAKSIAGGMPLGAVVGRKELMAALPKGGLGGTYSGNPISCAAALASLAQM-TDENLAT 313
           L  AK I GG P+ A++    +  AL  G  G TY GNP+ CA A   L  + T + L  
Sbjct: 250 LTSAKGIGGGFPIAAMLTIDRVAPALSVGTHGSTYGGNPLGCAVAERVLDIINTPQVLDG 309

Query: 314 WGERQEQAIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEAARA 373
            GERQ Q       R  A  L  +   + G G + G   A         Q  +VM  A+ 
Sbjct: 310 VGERQAQLTAGL--RILADELGVF-SEIRGQGLLIGAVLAER----WRGQAGQVMRLAQE 362

Query: 374 RGLLLMPSGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAEL 415
            GLL++ +G    ++RL   L I    + E L  +   L  L
Sbjct: 363 EGLLVLQAG--ADVVRLAPSLIIPEADIREALGRMRAALLRL 402


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: 423
Number of extensions: 20
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: 404
Length adjustment: 31
Effective length of query: 385
Effective length of database: 373
Effective search space:   143605
Effective search space used:   143605
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