GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araG in Pseudomonas fluorescens FW300-N2C3

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate AO356_00965 AO356_00965 sugar ABC transporter ATP-binding protein

Query= CharProtDB::CH_014279
         (504 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_00965
          Length = 517

 Score =  337 bits (864), Expect = 6e-97
 Identities = 194/473 (41%), Positives = 276/473 (58%), Gaps = 6/473 (1%)

Query: 8   LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67
           L   GIGKT+     LTDI+     G+V AL GENGAGKSTL KI+ G   PTTG +   
Sbjct: 10  LCVSGIGKTY-AQPVLTDINLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQFQ 68

Query: 68  GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127
           GQ+      T A   GV ++ QEL+L+P ++VAEN++L  LP  GG ++R  L   A   
Sbjct: 69  GQDYRPGSRTQAEELGVRMVMQELNLLPTLSVAENLFLDNLPSHGGWISRKQLRKAAIEA 128

Query: 128 LKHLGMD-IDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVI 186
           +  +G+D IDPDT +  L IG  QMVEIA+ L  +  ++  DEPT+ L+ARE++ LF  I
Sbjct: 129 MAQVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQI 188

Query: 187 RELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIG 246
             L+  G  I+Y+SHR+EE+  ++  I V +DG  V     M   D + LV  MVGR++G
Sbjct: 189 TRLQARGVAIIYISHRLEELARVAQRIAVLRDGNLV-CVEPMANYDSEQLVTLMVGRELG 247

Query: 247 DIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGT 306
           +     PR  G   L +  +        +S  VRSGEI G+ GL+GAGR+EL++ +FG  
Sbjct: 248 EHIDLGPRQIGAPALTVKGLTRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGAD 307

Query: 307 QITAGQVYIDQ--QPIDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHV 364
              +G V +    + + IR PS A+A G+ L  EDRK EG++   S+  NI +      +
Sbjct: 308 PADSGTVALGSPARVVSIRSPSDAVAHGIALITEDRKGEGLLLTQSIAANIALG-NMPEI 366

Query: 365 LGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLD 424
               ++N   E   A   + ++ I++    QL+  LSGGNQQK ++GRWL  +  V+L D
Sbjct: 367 SSAGLVNGSAELALAQRQVDAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCAVMLFD 426

Query: 425 EPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEI 477
           EPTRGIDVGAK +IY ++  L  QG A++  SSDL E++ + DRI V+  G +
Sbjct: 427 EPTRGIDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRL 479



 Score = 92.0 bits (227), Expect = 4e-23
 Identities = 70/249 (28%), Positives = 119/249 (47%), Gaps = 20/249 (8%)

Query: 11  RGIGKTFPGVKALT------DISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSV 64
           R IG     VK LT      D+SF+  +G++  + G  GAG++ LL+++ G     +G+V
Sbjct: 255 RQIGAPALTVKGLTRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGADPADSGTV 314

Query: 65  VING--QEMSFSDTTAALNAGVAIIYQELH---LVPEMTVAENIYLGQLPHKGGIVNRSL 119
            +    + +S    + A+  G+A+I ++     L+   ++A NI LG +P    I +  L
Sbjct: 315 ALGSPARVVSIRSPSDAVAHGIALITEDRKGEGLLLTQSIAANIALGNMPE---ISSAGL 371

Query: 120 LNYEAGLQLKHLGMDI------DPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSS 173
           +N  A L L    +D        P   +  LS G  Q V I + L R+  ++ FDEPT  
Sbjct: 372 VNGSAELALAQRQVDAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCAVMLFDEPTRG 431

Query: 174 LSAREIDNLFRVIRELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDH 233
           +      +++ ++ EL ++G+ ++ VS  + E+  + D I V   GR + TF        
Sbjct: 432 IDVGAKFDIYALLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGRLIDTFERDSWTQD 491

Query: 234 DALVQAMVG 242
           D L  A  G
Sbjct: 492 DLLAAAFAG 500


Lambda     K      H
   0.319    0.136    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: 682
Number of extensions: 28
Number of successful extensions: 10
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: 504
Length of database: 517
Length adjustment: 35
Effective length of query: 469
Effective length of database: 482
Effective search space:   226058
Effective search space used:   226058
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 (21.7 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