Alignments for a candidate for ytfR in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for ytfR in Cupriavidus basilensis 4G11

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate RR42_RS30800 RR42_RS30800 sugar ABC transporter ATP-binding protein

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



>FitnessBrowser__Cup4G11:RR42_RS30800
          Length = 530

 Score =  274 bits (701), Expect = 5e-78
 Identities = 173/486 (35%), Positives = 259/486 (53%), Gaps = 22/486 (4%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           ILR  G++K F  + A D++   L+RGE++ALLGENGAGKSTL+  L G Y AD GT+ +
Sbjct: 5   ILRLAGITKRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEV 64

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128
           +GQ + P     A   GIG V+Q   L  N+SV DN+ +G +P     L       +   
Sbjct: 65  DGQPLPPGQPRAALTAGIGMVHQHFTLADNLSVLDNIMLGTQPLWQWRLDGHAARGKVLA 124

Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188
           L   +G ++  +  +   SV  +Q V I +A+   A+VLILDEPTA L   E E LF  +
Sbjct: 125 LAERFGLAVRPQARVGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFSTL 184

Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELDT 248
            QL   G+S+IF++H LD+V +VSDRI VLR G  V      +  + EL ++M+GR +  
Sbjct: 185 AQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVGRVVAM 244

Query: 249 HALQRAGRTLLSD-------KPVAAFKNYGKKGT-----IAPFDLEVRPGEIVGLAGLLG 296
              +R  R    D        PV A ++ G +       +    L+VR GEIVG+AG+ G
Sbjct: 245 P--ERVARRSAEDGANGNAAPPVLALEHVGARAANGRALLREVSLQVRAGEIVGIAGVSG 302

Query: 297 SGRTETAEVIFGIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVR 356
           +G+   AE+  G+  A  G   + GKP + + P      G+   PEDR   G++   +V 
Sbjct: 303 NGQAALAELASGMLEASEGRITLAGKPMSAK-PRAWIGAGVARVPEDRHAIGVVGDLAVW 361

Query: 357 ENIILALQAQRGWLR--PISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLS 414
           EN +    ++  + R   I R   Q  A   + +  +RT   + P   +SGGN QK++L 
Sbjct: 362 ENAVSEQLSEPRFSRWGVIRRAAAQRFARDLVARFDVRTAGIDVPARTMSGGNMQKLILG 421

Query: 415 RWLLTR-----PQFLILDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYA 469
           R L  R     P+ ++  +PT G+D+GA A +   +     +G A+L+IS +L+EL   A
Sbjct: 422 RALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRARLLDAAREGAAVLLISEDLDELHALA 481

Query: 470 DRVIIM 475
           DR+ +M
Sbjct: 482 DRIAVM 487



 Score = 83.2 bits (204), Expect = 2e-20
 Identities = 69/238 (28%), Positives = 115/238 (48%), Gaps = 18/238 (7%)

Query: 268 KNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLR 327
           K +G         LE++ GE++ L G  G+G++    ++FG   AD+GT  + G+P    
Sbjct: 13  KRFGPLVANDDISLELQRGEVLALLGENGAGKSTLVSILFGHYVADAGTVEVDGQPLPPG 72

Query: 328 SPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGWLRP--ISRKEQQEIAERF 385
            P  A   GIG   +      +    SV +NI+L  Q    W      +R +   +AERF
Sbjct: 73  QPRAALTAGIGMVHQHFT---LADNLSVLDNIMLGTQPLWQWRLDGHAARGKVLALAERF 129

Query: 386 IRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLI 445
              L +R  +    +  LS G +Q+V + + L    + LILDEPT  +       +   +
Sbjct: 130 --GLAVRPQAR---VGELSVGERQRVEIVKALYRGARVLILDEPTAVLTPHEAETLFSTL 184

Query: 446 ETLCADGLALLVISSELEELVGYADRVIIMRDRKQVA--------EIPLAELSVPAIM 495
             L A+GL+++ IS +L+E++  +DR+ ++R  K VA        +  LAEL V  ++
Sbjct: 185 AQLIAEGLSVIFISHKLDEVLRVSDRIAVLRGGKLVALCAAAQTTKAELAELMVGRVV 242



 Score = 70.9 bits (172), Expect = 1e-16
 Identities = 61/251 (24%), Positives = 117/251 (46%), Gaps = 14/251 (5%)

Query: 21  GVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAH 80
           G   L  V   +R GEI+ + G +G G++ L +  +G+  A  G I L G+ +S K  A 
Sbjct: 278 GRALLREVSLQVRAGEIVGIAGVSGNGQAALAELASGMLEASEGRITLAGKPMSAKPRAW 337

Query: 81  AQQLGIGTVYQE---VNLLPNMSVADNLFIGR--EPK--RFGLLRRKEMEKRATELMASY 133
               G+  V ++   + ++ +++V +N    +  EP+  R+G++RR   ++ A +L+A +
Sbjct: 338 IGA-GVARVPEDRHAIGVVGDLAVWENAVSEQLSEPRFSRWGVIRRAAAQRFARDLVARF 396

Query: 134 GF-SLDVREPLNRFSVAMQQIVAICRAIDL-----SAKVLILDEPTASLDTQEVELLFDL 187
              +  +  P    S    Q + + RA+ +     + ++++  +PT  LD   V  +   
Sbjct: 397 DVRTAGIDVPARTMSGGNMQKLILGRALSVRGEGSAPRLVVASQPTWGLDIGAVAYVRAR 456

Query: 188 MRQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMMLGRELD 247
           +      G +++ ++  LD+++ ++DRI V+  G     R T      EL   M G    
Sbjct: 457 LLDAAREGAAVLLISEDLDELHALADRIAVMHAGHLTEARPTAAWTLGELGLAMAGSGGG 516

Query: 248 THALQRAGRTL 258
            HA    G  L
Sbjct: 517 QHAQAGKGEVL 527


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: 633
Number of extensions: 32
Number of successful extensions: 9
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: 530
Length adjustment: 35
Effective length of query: 465
Effective length of database: 495
Effective search space:   230175
Effective search space used:   230175
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