GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocE in Pseudomonas fluorescens FW300-N1B4

Align Amino-acid permease RocE (characterized)
to candidate Pf1N1B4_1580 Histidine transport protein (permease)

Query= SwissProt::P39137
         (467 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1580 Histidine transport
           protein (permease)
          Length = 469

 Score =  300 bits (767), Expect = 9e-86
 Identities = 152/453 (33%), Positives = 250/453 (55%), Gaps = 4/453 (0%)

Query: 5   QDNGNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLTM 64
           Q     L+R + +RH+  ++LG  IGTG F G+   I  AGP   +L+YL+GG  +F+ M
Sbjct: 2   QQPAKGLKRGLSARHIRFMALGSAIGTGLFYGSASAIQMAGP-AVLLAYLIGGAAVFMVM 60

Query: 65  LCLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWFP 124
             LGE+AV  PV+GSF  YA+ ++ P  GF  GW Y     +    +  + G  M  WFP
Sbjct: 61  RALGEMAVHNPVAGSFGQYASTYLGPMAGFILGWTYAFEMVIVGMADVTAFGIYMGFWFP 120

Query: 125 HIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILG-GAAMFGLIDLK 183
            +D WIW L   +++  LN    K F E EFW S +K+  I+  I+ G G  +FG+    
Sbjct: 121 EVDRWIWVLGIVSVVGGLNLCNVKVFGEMEFWLSLLKVAAIVAMILGGFGIMLFGISTAP 180

Query: 184 GGEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIK 243
           G +       +   G  PNG+  ++ +   V FAF G E+IGV AGE++DP++ +PR+I 
Sbjct: 181 GAQATDISNLWSHGGFMPNGVGGLIASFAVVMFAFGGIEIIGVTAGEAKDPQRVLPRAIN 240

Query: 244 QTVWRTLVFFVLSIIVIAGMIPWKQAGVVESPFVAVFEQIGIPYAADIMNFVILIALLSV 303
               R L+F+VL+++V+  + PW+Q G   SPFV +F+ +GI  AA I+N V++ A +S 
Sbjct: 241 AVPLRILLFYVLTMLVLMSIFPWQQIGSQGSPFVQIFDNLGISSAATILNIVVISAAVSA 300

Query: 304 ANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTKFAQAETVY 363
            NS ++ + R++Y +A +G A K   + ++ GVP  +++V  +   L +L  +   E V+
Sbjct: 301 INSDIFGAGRMMYGLAQQGHAPKGFARLSRNGVPWLTVVVMSSALLLGVLLNYLIPENVF 360

Query: 364 MVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLIGLTLNTVV 423
           +++ S+A  +    W+ I  +Q+  RR    E  ++  LKF  P +P  P+  +     +
Sbjct: 361 LLIASVATFATVWVWLMILFTQVAMRRSMSAE--QVAQLKFPVPFWPYAPMAAIAFMLFI 418

Query: 424 LISLAFDPEQRIALYCGVPFMIICYIIYHVVIK 456
              L + P+ + AL  GV ++++  + Y   +K
Sbjct: 419 FGVLGYFPDTQAALIVGVVWIVLLVLAYLTWVK 451


Lambda     K      H
   0.329    0.142    0.438 

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: 548
Number of extensions: 29
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: 467
Length of database: 469
Length adjustment: 33
Effective length of query: 434
Effective length of database: 436
Effective search space:   189224
Effective search space used:   189224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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