GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lysP in Pseudomonas fluorescens FW300-N2C3

Align S-adenosylmethionine permease SAM3 (characterized)
to candidate AO356_11625 AO356_11625 GABA permease

Query= CharProtDB::CH_091257
         (587 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_11625
          Length = 464

 Score =  201 bits (510), Expect = 7e-56
 Identities = 128/421 (30%), Positives = 212/421 (50%), Gaps = 17/421 (4%)

Query: 77  LSQRHLTMIAIGGTLGTGLFIGLGYSLASGPAALLIGFLLVGTSMFCVVQSAAELSCQFP 136
           L  RH+TM++I G +G GLF+G G+++A+   A+L+ +   G  +  V++   E++   P
Sbjct: 14  LKPRHVTMLSIAGVIGAGLFVGSGHAIAAAGPAVLLAYAAAGALVVLVMRMLGEMAVASP 73

Query: 137 VSGSYATHVSRFIDESVGFTVATNYALAWLISFPSELIGCALTISYWNQTVNPAVWVAIF 196
            +GS++T+  R I    GFT+   Y   W++  P E    A  +  W   V   V+  + 
Sbjct: 74  DTGSFSTYADRAIGHWAGFTIGWLYWWFWVLVIPLEANAAATILHAWFPNVAIWVFTLVI 133

Query: 197 YVFIMVLNLFGVRGFAETEFALSIIKVIAIFIFIIIGIVLIAGGGPNSTGYIGAKYWHDP 256
            + + V NLF V+ + E EF  +++KV+AI  FI +G++ I G  P S    G  +  D 
Sbjct: 134 TLLLTVTNLFSVKNYGEFEFWFALVKVVAIIGFIGLGLMAIFGVLPTSQ-VSGVSHLFDT 192

Query: 257 GAFAKPVFKNLCNTFVSAAFSFGGSELVLLTSTESKNI-SAISRAAKGTFWRIAIFYITT 315
             F       +    ++  FSF G+E+V + + ESKN    IS+A     WRI +FY+ +
Sbjct: 193 QGFLPNGMGAVLGAILTTMFSFMGTEIVTIAAAESKNPGQQISKATNSVIWRIGLFYLVS 252

Query: 316 VVIIGCLVPYNDPRLLSGSNSEDVSASPFVIALSNTGSMGAKVSNFMNVVILVAVVSVCN 375
           + I+  LVP+NDP L S  + + V        L   G   AK+   +++V+LVAV S  N
Sbjct: 253 IFIVVALVPWNDPLLASVGSYQTV--------LERMGIPNAKL--IVDIVVLVAVTSCLN 302

Query: 376 SCVYASSRLIQALGASGQLPSVCSYMDRKGRPLVGIGISGAFGLLGFLVASKKEDEVFTW 435
           S +Y +SR++ +LG  G  P+V    ++ G P   + +S     L           VF +
Sbjct: 303 SALYTASRMMFSLGKRGDAPAVSQRTNKSGTPHWAVMLSTGAAFLAVFANYVAPAAVFEF 362

Query: 436 LFALCSISSFFTWFCICMSQIRFRMALKAQGRSNDEIAYKSIL--GVYGGILGCVLNALL 493
           L A     +   +  I +SQ+R R    A+G   ++IA+   L  G+   ++  ++ AL 
Sbjct: 363 LLASSGAIALLVYLVIAVSQLRMRKQRMARG---EKIAFSMWLFPGLTYAVIVFIVGALT 419

Query: 494 I 494
           I
Sbjct: 420 I 420


Lambda     K      H
   0.324    0.138    0.417 

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: 577
Number of extensions: 30
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: 587
Length of database: 464
Length adjustment: 35
Effective length of query: 552
Effective length of database: 429
Effective search space:   236808
Effective search space used:   236808
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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