Alignments for a candidate for ytfR in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Pseudomonas fluorescens GW456-L13

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121
          Length = 514

 Score =  340 bits (873), Expect = 5e-98
 Identities = 188/497 (37%), Positives = 300/497 (60%), Gaps = 21/497 (4%)

Query: 10  LRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLE 69
           LR  G+ K FPGVKALDN+ F    G++ AL+GENGAGKSTL+K L G Y    G + + 
Sbjct: 16  LRFNGIGKTFPGVKALDNISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPCSGALQIG 75

Query: 70  GQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATEL 129
            + +  K+TA +   G+  ++QE++L+P M+VA+NLF+G  P  FGL+ R  + ++A   
Sbjct: 76  ERTMDFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRSTLRQQALAC 135

Query: 130 MASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMR 189
           +      +D +E + R S+  +Q+V I +A+   A V+  DEPT+SL  +E++ L  ++ 
Sbjct: 136 LKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIG 195

Query: 190 QLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGC-RETCELPQIELVKMMLGREL-- 246
           +LRD G  +++V+H +++V+++ + +TV ++G +V    +  +L   +LV  M+GR++  
Sbjct: 196 RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMSQLTHDQLVTCMVGRDIQD 255

Query: 247 --DTHALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAE 304
             D    QR    L  D  +         G   P   EV  GEI+GL GL+G+GRTE   
Sbjct: 256 IYDYRPRQRGAVALKVDGLLG-------PGLREPVSFEVHKGEILGLFGLVGAGRTELLR 308

Query: 305 VIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQ 364
           ++ G+    +G   ++G    LRSP  A   GI  CPEDRK +GI+  ASV ENI ++ +
Sbjct: 309 LLSGLARHSAGQLKLRGHELKLRSPRDAIAAGILLCPEDRKKEGILPLASVAENINISAR 368

Query: 365 AQRGWLRPISR-KEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQF 423
                   + R   +++ AE+ I+ L ++TP+  Q I +LSGGNQQK +L RWL    + 
Sbjct: 369 GAHSTFGCLLRGLWEKDNAEQQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKV 428

Query: 424 LILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRD------ 477
           L+LDEPTRGID+GA AEI ++I  L A+G+A++V+SS+L E++G +DR++++ +      
Sbjct: 429 LLLDEPTRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVLCEGALRGE 488

Query: 478 --RKQVAEIPLAELSVP 492
             R+Q  E  L +L++P
Sbjct: 489 LSREQANESNLLQLALP 505



 Score = 84.3 bits (207), Expect = 9e-21
 Identities = 72/246 (29%), Positives = 120/246 (48%), Gaps = 17/246 (6%)

Query: 10  LRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLE 69
           L+ +GL    PG++  + V F + +GEI+ L G  GAG++ L++ L+G+     G + L 
Sbjct: 269 LKVDGL--LGPGLR--EPVSFEVHKGEILGLFGLVGAGRTELLRLLSGLARHSAGQLKLR 324

Query: 70  GQAI---SPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKR--FGLLRRKEMEK 124
           G  +   SP++   A  L      ++  +LP  SVA+N+ I        FG L R   EK
Sbjct: 325 GHELKLRSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEK 384

Query: 125 RATELMASYGFSLDVREP-----LNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQ 179
              E       +L V+ P     +   S   QQ   + R + +  KVL+LDEPT  +D  
Sbjct: 385 DNAEQQIK---ALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIG 441

Query: 180 EVELLFDLMRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVK 239
               ++ ++  L   G+++I V+  L +V  +SDRI VL  G+  G     +  +  L++
Sbjct: 442 AKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVLCEGALRGELSREQANESNLLQ 501

Query: 240 MMLGRE 245
           + L R+
Sbjct: 502 LALPRQ 507


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: 606
Number of extensions: 29
Number of successful extensions: 7
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: 514
Length adjustment: 34
Effective length of query: 466
Effective length of database: 480
Effective search space:   223680
Effective search space used:   223680
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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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