Alignments for a candidate for ytfR in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Pseudomonas putida KT2440

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate PP_2759 PP_2759 ribose ABC transporter - ATP-binding subunit

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



>FitnessBrowser__Putida:PP_2759
          Length = 512

 Score =  301 bits (771), Expect = 4e-86
 Identities = 176/472 (37%), Positives = 264/472 (55%), Gaps = 12/472 (2%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           +L   G+ K F   +ALD     +  G +  L+GENGAGKSTLIK L G++  D G++ L
Sbjct: 5   VLELRGIVKTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLLL 64

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFG-LLRRKEMEKRAT 127
           +GQ     +    ++LGIG ++QE  L    +V + LF G E +RFG LL R+  ++ A 
Sbjct: 65  DGQPHGHFSPRQVERLGIGFIHQERLLPARFTVGEALFFGHE-RRFGPLLDRRSQQREAA 123

Query: 128 ELMASY-GFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFD 186
            L+  Y G  L     +   S A QQ+V I RA+ +  +VL+ DEP+ +L  +EVE L  
Sbjct: 124 RLLDDYFGLRLPANALIGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLLR 183

Query: 187 LMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRE- 245
           ++++LRD G+++++++H+L ++  + DR+TVLRNG  V           ++ ++M+ RE 
Sbjct: 184 IVQRLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQITRLMVNREV 243

Query: 246 --LDTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETA 303
             L       AG  LL        +  G+       DL+VR GEIVGL GL+GSG  E  
Sbjct: 244 GELYPKVAVPAGALLLD------VRGLGRARAYQGIDLQVRRGEIVGLTGLVGSGAKELL 297

Query: 304 EVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILAL 363
             +FG+ P DSG   + G+P +LRSP +A   G+   PE+R+  G+    SV+EN  LA 
Sbjct: 298 RSLFGLAPPDSGEVRLDGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAA 357

Query: 364 QAQRGWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQF 423
            ++   L  +S   ++      I +L I+       +  LSGGNQQKV L++W       
Sbjct: 358 LSRFVRLGLLSPARERHTTLELIERLRIKAHGAHAKVRQLSGGNQQKVALAKWFARCSSL 417

Query: 424 LILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIM 475
            +LDEP+ GIDVGA  EI RLI  L  +G  +L++SS+L EL+G  DR+ +M
Sbjct: 418 YLLDEPSVGIDVGAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVM 469



 Score =  105 bits (263), Expect = 3e-27
 Identities = 73/228 (32%), Positives = 118/228 (51%), Gaps = 7/228 (3%)

Query: 268 KNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLR 327
           K +G    +    L V  G + GL G  G+G++   +V+ GI   D+G+ L+ G+P    
Sbjct: 13  KTFGATRALDGASLRVAAGSVHGLVGENGAGKSTLIKVLAGIHRPDAGSLLLDGQPHGHF 72

Query: 328 SPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGWLRPISRKEQQEIAERFIR 387
           SP Q   LGIGF  ++R    + A  +V E +    + + G L  + R+ QQ  A R + 
Sbjct: 73  SPRQVERLGIGFIHQERL---LPARFTVGEALFFGHERRFGPL--LDRRSQQREAARLLD 127

Query: 388 Q-LGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIE 446
              G+R P+    I  LS   QQ V + R LL +P+ L+ DEP+  +       ++R+++
Sbjct: 128 DYFGLRLPANAL-IGELSSAEQQMVQIVRALLIKPRVLVFDEPSVALVQREVERLLRIVQ 186

Query: 447 TLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAELSVPAI 494
            L  DGLA++ IS  L+E+    DRV ++R+ + VAE+     S+  I
Sbjct: 187 RLRDDGLAIVYISHYLQEIEALCDRVTVLRNGRDVAEVSPRNTSLEQI 234



 Score = 71.6 bits (174), Expect = 6e-17
 Identities = 57/224 (25%), Positives = 106/224 (47%), Gaps = 18/224 (8%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           +L   GL +     +A   +D  +RRGEI+ L G  G+G   L+++L G+   D G + L
Sbjct: 258 LLDVRGLGR----ARAYQGIDLQVRRGEIVGLTGLVGSGAKELLRSLFGLAPPDSGEVRL 313

Query: 69  EGQAISPKNTAHAQQLGIGTVYQE---VNLLPNMSVADNLFIGREPK--RFGLLRRKEME 123
           +GQ +S ++   A   G+  + +E     +  ++SV +N  +    +  R GLL      
Sbjct: 314 DGQPLSLRSPREAVAQGVALMPEERRRQGVALDLSVQENTTLAALSRFVRLGLLSPARER 373

Query: 124 KRATELMA-----SYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDT 178
               EL+      ++G    VR+     S   QQ VA+ +     + + +LDEP+  +D 
Sbjct: 374 HTTLELIERLRIKAHGAHAKVRQ----LSGGNQQKVALAKWFARCSSLYLLDEPSVGIDV 429

Query: 179 QEVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGS 222
                ++ L+ +L   G  ++ ++  L ++  + DRI V+  G+
Sbjct: 430 GAKVEIYRLIGELVKEGAGVLILSSDLPELIGLCDRIHVMHRGA 473


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: 602
Number of extensions: 33
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 500
Length of database: 512
Length adjustment: 34
Effective length of query: 466
Effective length of database: 478
Effective search space:   222748
Effective search space used:   222748
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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