GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysP in Pseudomonas fluorescens FW300-N1B4

Align Probable lysine/arginine permease CAN3; Basic amino acids permease CAN3 (characterized)
to candidate Pf1N1B4_5139 Gamma-aminobutyrate permease

Query= SwissProt::A0A1D8PPG4
         (566 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5139
          Length = 501

 Score =  209 bits (531), Expect = 3e-58
 Identities = 136/443 (30%), Positives = 218/443 (49%), Gaps = 28/443 (6%)

Query: 44  DRITEYDSHGEVKRDLKARHVAMIGIGSTIGTGLFISTGHLLSQTGPVMSLISFLFVTTI 103
           + +   DS+G++ +  K RHV M+ I   IG GLF+ +GH ++  GP + L+++LF   +
Sbjct: 35  NNLNSRDSNGQLAQGFKPRHVTMLSIAGIIGAGLFVGSGHAIAAAGPAV-LLAYLFSGLL 93

Query: 104 CFSVTQSLGEMATYIPVSGSFVQFITRWVSKSCGAANGWLYGWSWAITFGLELSIVGQVI 163
              V + LGEMA   P +GSF  +  + + +  G   GWLY W W +   +E    G V+
Sbjct: 94  VVLVMRMLGEMAVANPDTGSFSTYADQAIGRWAGFTIGWLYWWFWVLVIPIEALAAGHVL 153

Query: 164 QFWTDAIPLAAWISIFFVLLTALNLFPVKFYGEIEFWMASIKLTAVIGWIIYAFCMVCGA 223
             W   I    +     +LL   NLF V  YGE EFW A  K+ A+IG+I   F ++ G 
Sbjct: 154 NQWFPQIDTWLFALTSIILLVVTNLFSVSKYGEFEFWFAMAKVVAIIGFIGLGFAVLMG- 212

Query: 224 GKTGPVGFRYWRNGYAWGDGMIVSNNGKYA----IAFINGLINAVFTFQGTELVAITAGE 279
                    +     A G   ++  +G +A     A +   I  +F+F GTE V I A E
Sbjct: 213 ---------WIPEREASGLSRLMEEHGGFAPNGLSAVVGAFITIMFSFIGTEAVTIAAAE 263

Query: 280 ASPKA--LKSAIRKVMFRILVFYVLCMLFIGLLVPYNDPKLTEDGGFTRNSPFLIAMENS 337
           +S  A  +  A R V++RI VFY+L +  +  +VP+NDP L   G + R      A+E  
Sbjct: 264 SSNPAQNIAKATRSVIWRIGVFYLLSIFVVISVVPWNDPLLASVGSYQR------ALELM 317

Query: 338 GTKVLPHIFNAVIVTTIISAGNSTVYAGSRIFYGLAESGVAPKIFLSTTKAGVPYVAVLF 397
                  + + V++  + S  NS++Y  SR+ + L + G APK    T+  GVP  AV+ 
Sbjct: 318 NIPHAKLMVDVVVLIAVASCMNSSIYIASRMLFSLGKRGDAPKPLKVTSSDGVPRAAVIA 377

Query: 398 TAAFGALGYLVVSNDGTVVFNWLLNIAATAGLVAWGFISVSHIRFMQVLKQRGISRDTLP 457
           +   GA   L        +F +LL  +    L+ +  I+VS +R  ++L ++ +   TL 
Sbjct: 378 STVLGAGVTLFSYFMPAGLFQFLLASSGAIALLVYLVIAVSQLRMRKILLRQNV---TLT 434

Query: 458 FKAFFMPYSAYYAAIVVFTVALI 480
           FK +  P+  +   ++ F  A +
Sbjct: 435 FKMWLFPWLTW--LVIAFICAAL 455


Lambda     K      H
   0.327    0.141    0.451 

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: 745
Number of extensions: 43
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: 566
Length of database: 501
Length adjustment: 35
Effective length of query: 531
Effective length of database: 466
Effective search space:   247446
Effective search space used:   247446
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 (21.7 bits)
S2: 52 (24.6 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:

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