GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Miya:8502321
          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.

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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:

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:

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