GapMind for catabolism of small carbon sources

 

Aligments for a candidate for lysN in Pseudomonas fluorescens FW300-N2E2

Align L-2-aminoadipate aminotransferase monomer (EC 2.6.1.39) (characterized)
to candidate Pf6N2E2_5813 Transcriptional regulator, GntR family domain / Aspartate aminotransferase (EC 2.6.1.1)

Query= metacyc::MONOMER-6727
         (397 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5813 Transcriptional
           regulator, GntR family domain / Aspartate
           aminotransferase (EC 2.6.1.1)
          Length = 388

 Score =  242 bits (617), Expect = 2e-68
 Identities = 148/394 (37%), Positives = 217/394 (55%), Gaps = 18/394 (4%)

Query: 9   AFGKSAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVAL 68
           AF +   R+++S IRE+L   QRP ++SFAGGLPA  + PK E A     +         
Sbjct: 2   AFSERVSRLKSSLIREILAAAQRPEVMSFAGGLPAEAMLPKVEWAAMPLSMG-------- 53

Query: 69  QYSPTEGYAPLR---AFVAEWIGVRPE--EVLITTGSQQALDLVGKVFLDEGSPVLLEAP 123
           QY  +EG   LR   A  A  +GV  E  +VL+ +GSQQ LDL  K+ +D G+ V+LEAP
Sbjct: 54  QYGMSEGEPALREALAAQARALGVACEASQVLVVSGSQQTLDLAAKLHIDVGTEVMLEAP 113

Query: 124 SYMGAIQAFRLQGPRFLTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLP 183
           +Y+ A+Q F+L G   +TVP   +GPDL AL   L+R RP F+YLIP+FQNP+       
Sbjct: 114 TYLAALQIFQLFGADCITVPLEADGPDLKALRARLERHRPAFIYLIPTFQNPSAVRYSEA 173

Query: 184 ARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFSKVLSPG 243
            R  +  ++ E G+ ++ED+ YREL F       +    R+A +   IY G+ SK L PG
Sbjct: 174 KRDAVAALLDEFGVTLIEDEPYRELTFDGGSATPIVSRLRKASW---IYTGTVSKTLLPG 230

Query: 244 LRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELL-KEGFSERLERVRRVYREKAQ 302
           LRV + +A P+    L++ KQ ADLHT  + Q    + +  E +   L  +R  YR++  
Sbjct: 231 LRVGYLIASPDLFPHLLRLKQSADLHTNRIGQWQALQWIGTEQYRRHLSELRDFYRDRRD 290

Query: 303 AMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGG 362
               AL++       +  P+GG+F W+ L + L    L   AL  +VAF+PG PFF    
Sbjct: 291 RFQAALEKHFTDLADWNIPQGGLFFWLTLKQPLDTRTLLAAALAADVAFMPGEPFFPEPD 350

Query: 363 GE-NTLRLSYATLDREGIAEGVRRLGRALKGLLA 395
                LRL+++ +D   + EG++RL   ++  LA
Sbjct: 351 QHPGHLRLNFSHIDPARLDEGLKRLAGVVREALA 384


Lambda     K      H
   0.320    0.139    0.401 

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: 403
Number of extensions: 19
Number of successful extensions: 5
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: 397
Length of database: 388
Length adjustment: 31
Effective length of query: 366
Effective length of database: 357
Effective search space:   130662
Effective search space used:   130662
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 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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