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

GapMind for catabolism of small carbon sources

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

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate Pf1N1B4_4286 Inositol transport system ATP-binding protein

Query= ecocyc::YTFR-MONOMER
         (500 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4286
          Length = 526

 Score =  356 bits (914), Expect = e-102
 Identities = 189/492 (38%), Positives = 300/492 (60%), Gaps = 12/492 (2%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           +L    +SK FPGV AL +V   +R G ++AL+GENGAGKSTL+K + G+Y  D G + L
Sbjct: 32  LLEIINVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDAGELRL 91

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKR-FGLLRRKEMEKRAT 127
            G+ +  +    A Q GI  ++QE+NL+P+MS+A+N++IGRE      ++  +EM +   
Sbjct: 92  RGKPVVFETPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMIDHREMHRCTA 151

Query: 128 ELMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDL 187
           +L+     +LD  E +   S+A +Q+V I +A+   + +LI+DEPT+++  +EV  LF +
Sbjct: 152 KLLERLRINLDPEELVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITDKEVAHLFSI 211

Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELD 247
           +  L+ +G  +I++TH +++V+ ++D + V R+G+++G +    +    L+ MM+GREL 
Sbjct: 212 IADLKRQGKGIIYITHKMNEVFSIADEVAVFRDGAYIGLQRADSMDGDSLISMMVGRELS 271

Query: 248 THALQRAGRTLLSDKPVA----AFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETA 303
                R       +KP+     + ++    G       ++  GEI+G+AGL+GSGRT  A
Sbjct: 272 QLFPVR-------EKPIGDLLLSVRDLKLDGIFKDVSFDLHAGEILGIAGLMGSGRTNVA 324

Query: 304 EVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILAL 363
           E IFGI P+D G   + G+   +  PH A   G     EDRK  G+    SV EN+ +A+
Sbjct: 325 EAIFGITPSDGGEIRLDGEVVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAV 384

Query: 364 QAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQF 423
                    I +K  + + E   ++L ++TPS EQ I+ LSGGNQQK LL+RWL+T P+ 
Sbjct: 385 LPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRI 444

Query: 424 LILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRKQVAE 483
           LILDEPTRGIDVGA AEI RLI  L ++G+A+++ISSEL E++G +DRV++M +   +  
Sbjct: 445 LILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHEGDLMGT 504

Query: 484 IPLAELSVPAIM 495
           +  +E +   +M
Sbjct: 505 LDRSEATQERVM 516



 Score = 81.6 bits (200), Expect = 6e-20
 Identities = 53/223 (23%), Positives = 110/223 (49%), Gaps = 6/223 (2%)

Query: 27  NVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQLGI 86
           +V F L  GEI+ + G  G+G++ + +A+ G+  +D G I L+G+ +   +   A + G 
Sbjct: 299 DVSFDLHAGEILGIAGLMGSGRTNVAEAIFGITPSDGGEIRLDGEVVRISDPHMAIEKGF 358

Query: 87  GTVYQE---VNLLPNMSVADNLFIGREPKRFG--LLRRKEMEKRATELMASYGFSL-DVR 140
             + ++     L P +SV +N+ +   P   G   +++K +     ++          + 
Sbjct: 359 ALLTEDRKLSGLFPCLSVLENMEMAVLPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLE 418

Query: 141 EPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGVSLIF 200
           + ++  S   QQ   + R +  + ++LILDEPT  +D      ++ L+  L   G+++I 
Sbjct: 419 QCIDTLSGGNQQKALLARWLMTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIM 478

Query: 201 VTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLG 243
           ++  L +V  +SDR+ V+  G  +G  +  E  Q  ++++  G
Sbjct: 479 ISSELPEVLGMSDRVMVMHEGDLMGTLDRSEATQERVMQLASG 521


Lambda     K      H
   0.321    0.138    0.391 

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: 583
Number of extensions: 28
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 500
Length of database: 526
Length adjustment: 35
Effective length of query: 465
Effective length of database: 491
Effective search space:   228315
Effective search space used:   228315
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: 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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Steps (tab-delimited)
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Protein sequences (fasta format)
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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
the source code
instructions for running GapMind on your computer

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