GapMind for catabolism of small carbon sources

 

Aligments for a candidate for araG in Pseudomonas fluorescens FW300-N2E2

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate Pf6N2E2_162 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= CharProtDB::CH_014279
         (504 letters)



>lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_162 Ribose ABC transport
           system, ATP-binding protein RbsA (TC 3.A.1.2.1)
          Length = 517

 Score =  335 bits (859), Expect = 2e-96
 Identities = 193/473 (40%), Positives = 277/473 (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  GQDYRPGSRTQAEELGVRMVMQELNLLPTLSVAENLFLDNLPNHGGWISRKQLRKAAIEA 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   + + LV  MVGR++G
Sbjct: 189 TRLQARGVSIIYISHRLEELARVAQRIAVLRDGNLV-CVEPMANYNSEQLVTLMVGRELG 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 +    Q + IR P+ A+A G+ L  EDRK EG++   S+  NI +      +
Sbjct: 308 TADSGTVALGSPAQVVSIRSPADAVAHGIALITEDRKGEGLLLTQSIAANIALG-NMPEI 366

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

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



 Score = 94.4 bits (233), Expect = 9e-24
 Identities = 71/249 (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 RQIGAPALTVKGLTRSDKVRDVSFEVRSGEIFGISGLIGAGRTELLRLIFGADTADSGTV 314

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

Query: 120 LNYEAGLQLKHLGMDI------DPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSS 173
           +N +A L L    +D        P   +  LS G  Q V I + L R+  ++ FDEPT  
Sbjct: 372 VNGDAELALAQRQVDAMRIRSSSPTQLVSELSGGNQQKVVIGRWLERDCAVMLFDEPTRG 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: 671
Number of extensions: 27
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 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