GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ytfR in Desulfovibrio vulgaris Miyazaki F

Align galactofuranose ABC transporter putative ATP binding subunit (EC 7.5.2.9) (characterized)
to candidate 8502321 DvMF_3029 ABC transporter related (RefSeq)

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



>lcl|FitnessBrowser__Miya:8502321 DvMF_3029 ABC transporter related
           (RefSeq)
          Length = 537

 Score =  236 bits (602), Expect = 1e-66
 Identities = 151/469 (32%), Positives = 247/469 (52%), Gaps = 10/469 (2%)

Query: 9   ILRTEGLSKFFPGVKALDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWL 68
           ++R +G+ K F  V+A  ++   +R G I ALLGENGAGKSTL+  L G    D GTI +
Sbjct: 29  VVRLDGICKSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVV 88

Query: 69  EGQAISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPKRFGLLRRKEMEKRATE 128
           +G      +   A + GIG VYQ   L+ +M+VA+N+ +G+ P    LLR   M      
Sbjct: 89  DGVPTVFASPRDALRAGIGMVYQHFMLVDSMTVAENVLLGQSPDM--LLRPARMRDEVAA 146

Query: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLM 188
           L   YG ++D    +   S+  +Q V I + +   ++VLILDEPTA L  +E + LF+ M
Sbjct: 147 LAERYGLAVDPAARVGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEAM 206

Query: 189 RQLRDRGVSLIFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELP-QIELVKMMLGRELD 247
            ++ D+G +L+F++H L +V  V+D I +LR G  V      ++P Q  L   M+GR++ 
Sbjct: 207 WRMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADVPNQTVLANRMVGRDV- 265

Query: 248 THALQRAGRTLLSDKPVAAFKNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIF 307
              LQ   + L     V + ++    G ++   L+VR GEIV +AG+ G+G+ E  E I 
Sbjct: 266 --VLQVDAKRLTPVDTVLSVEHLSGAG-LSDVSLQVRRGEIVAIAGVAGNGQKELVEAIC 322

Query: 308 GIKPADSGTALIKGKPQNLRSPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQR 367
           G+   ++G   I G+P            G+ + PEDR+         + +N +L  + Q 
Sbjct: 323 GLARPEAGEVRILGRPWREFFAGPPGRRGLAYIPEDRQGLATCRHLDLVDNFLLTTRNQF 382

Query: 368 GWLRPISRKEQQEIAERFIRQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILD 427
                + R E     +R + +  ++      P   LSGGN QK+++ R    +P+ ++ +
Sbjct: 383 AKGVFLDRTEATNAVKRVVWEYNVQPGDITAPARALSGGNLQKLVIGREFFRKPEVIVAE 442

Query: 428 EPTRGIDVGAHAEII-RLIETLCADGLALLVISSELEELVGYADRVIIM 475
            PT+G+D+ A  E+  RL+E     G  +L+++ +L E +  ADR+ +M
Sbjct: 443 NPTQGLDISATEEVWGRLLEARSTSG--VLLVTGDLNEALELADRIAVM 489



 Score = 80.1 bits (196), Expect = 2e-19
 Identities = 65/223 (29%), Positives = 110/223 (49%), Gaps = 10/223 (4%)

Query: 268 KNYGKKGTIAPFDLEVRPGEIVGLAGLLGSGRTETAEVIFGIKPADSGTALIKGKPQNLR 327
           K++GK        L++RPG I  L G  G+G++    ++ G    D+GT ++ G P    
Sbjct: 37  KSFGKVRANHDITLDIRPGCIKALLGENGAGKSTLMSILAGKLRQDAGTIVVDGVPTVFA 96

Query: 328 SPHQASVLGIGFCPEDRKTDGIIAAASVRENIILALQAQRGWLRPIS-RKEQQEIAERFI 386
           SP  A   GIG   +      ++ + +V EN++L  Q+    LRP   R E   +AER+ 
Sbjct: 97  SPRDALRAGIGMVYQHFM---LVDSMTVAENVLLG-QSPDMLLRPARMRDEVAALAERY- 151

Query: 387 RQLGIRTPSTEQPIEFLSGGNQQKVLLSRWLLTRPQFLILDEPTRGIDVGAHAEIIRLIE 446
              G+      + +  LS G +Q+V + + L    + LILDEPT  +      ++   + 
Sbjct: 152 ---GLAVDPAAR-VGGLSMGERQRVEILKLLYRDSRVLILDEPTAVLTPRETDQLFEAMW 207

Query: 447 TLCADGLALLVISSELEELVGYADRVIIMRDRKQVAEIPLAEL 489
            +   G AL+ IS +L+E++  AD + I+R  + V E   A++
Sbjct: 208 RMADQGKALVFISHKLQEVLTVADEIAILRRGEVVDEFSEADV 250



 Score = 59.7 bits (143), Expect = 3e-13
 Identities = 47/224 (20%), Positives = 100/224 (44%), Gaps = 7/224 (3%)

Query: 25  LDNVDFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGTIWLEGQAISPKNTAHAQQL 84
           L +V   +RRGEI+A+ G  G G+  L++A+ G+   + G + + G+           + 
Sbjct: 291 LSDVSLQVRRGEIVAIAGVAGNGQKELVEAICGLARPEAGEVRILGRPWREFFAGPPGRR 350

Query: 85  GIGTVYQEVNLLP---NMSVADNLFIGREPK--RFGLLRRKEMEKRATELMASYGFSL-D 138
           G+  + ++   L    ++ + DN  +    +  +   L R E       ++  Y     D
Sbjct: 351 GLAYIPEDRQGLATCRHLDLVDNFLLTTRNQFAKGVFLDRTEATNAVKRVVWEYNVQPGD 410

Query: 139 VREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVELLFDLMRQLRDRGVSL 198
           +  P    S    Q + I R      +V++ + PT  LD    E ++  + + R     +
Sbjct: 411 ITAPARALSGGNLQKLVIGREFFRKPEVIVAENPTQGLDISATEEVWGRLLEARSTS-GV 469

Query: 199 IFVTHFLDQVYQVSDRITVLRNGSFVGCRETCELPQIELVKMML 242
           + VT  L++  +++DRI V+  G F+   +  +  +++ + +M+
Sbjct: 470 LLVTGDLNEALELADRIAVMYRGRFIDVFDKDDTAKVQAIGLMM 513


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: 627
Number of extensions: 41
Number of successful extensions: 8
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: 537
Length adjustment: 35
Effective length of query: 465
Effective length of database: 502
Effective search space:   233430
Effective search space used:   233430
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.

Links

Downloads

Related tools

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:

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:

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:

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