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

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources