GapMind for catabolism of small carbon sources

 

Aligments for a candidate for araG in Pseudomonas putida KT2440

Align L-arabinose ABC transporter, ATP-binding protein AraG; EC 3.6.3.17 (characterized)
to candidate PP_2455 PP_2455 ribose ABC transporter - ATP-binding subunit

Query= CharProtDB::CH_014279
         (504 letters)



>lcl|FitnessBrowser__Putida:PP_2455 PP_2455 ribose ABC transporter -
           ATP-binding subunit
          Length = 524

 Score =  340 bits (871), Expect = 9e-98
 Identities = 195/491 (39%), Positives = 293/491 (59%), Gaps = 6/491 (1%)

Query: 8   LSFRGIGKTFPGVKALTDISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVIN 67
           L+  G+GKT+     L ++S    AG+V AL GENGAGKSTL K++SG   PTTG +   
Sbjct: 17  LAASGLGKTY-AQPVLGEVSLSLRAGEVLALTGENGAGKSTLSKLISGLEVPTTGHMTYR 75

Query: 68  GQEMSFSDTTAALNAGVAIIYQELHLVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQ 127
           GQ  +      A   GV ++ QEL+L+P +TVAEN++L  LP + G ++   L   A   
Sbjct: 76  GQAYAPGSRGEAERLGVRMVMQELNLLPTLTVAENLFLDNLPSRFGWISHKRLRQLATAA 135

Query: 128 LKHLGMD-IDPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVI 186
           +  +G+D IDPDTP+  L IG  QMVEIA+ L  +  ++  DEPT+ L+ARE+  LF  I
Sbjct: 136 MARVGLDAIDPDTPVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVALLFTQI 195

Query: 187 RELRKEGRVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVGRDIG 246
             LR  G  I+Y+SHR+EE+  ++  I V +DG+ V     +Q+     LV  MVGR++G
Sbjct: 196 ERLRARGVAIVYISHRLEELQRVAQRIVVLRDGKLVCD-EPIQRYSSAELVNLMVGRELG 254

Query: 247 DIYGWQPRSYGEERLRLDAVKAPGVRTPISLAVRSGEIVGLFGLVGAGRSELMKGMFGGT 306
           +      R  G   L++D +        +S  VR+GEI G+ GL+GAGR+EL++ ++G  
Sbjct: 255 EHIDLGRRQLGAPLLKVDKLCRGDKVREVSFEVRAGEIFGISGLIGAGRTELLRLIYGAD 314

Query: 307 QITAGQVYIDQQP--IDIRKPSHAIAAGMMLCPEDRKAEGIIPVHSVRDNINISARRKHV 364
           +  +G + + Q P  + I  P  A+ AG+ L  EDRK EG++   S+  NI +       
Sbjct: 315 RADSGGIALGQPPQAVSIDSPKAAVRAGIALITEDRKGEGLLLTQSISANIALGNLGAVS 374

Query: 365 LGGCVINNGWEENNADHHIRSLNIKTPGAEQLIMNLSGGNQQKAILGRWLSEEMKVILLD 424
             G V+++  E+  A+  I+++ I++ GA+Q++  LSGGNQQK ++GRWL  + +V+L D
Sbjct: 375 RAG-VLDSEAEKALAERQIQAMRIRSAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFD 433

Query: 425 EPTRGIDVGAKHEIYNVIYALAAQGVAVLFASSDLPEVLGVADRIVVMREGEIAGELLHE 484
           EPTRGIDVGAK +IY ++  LA QG A++  SSDL E++ + DRI V+  G +      +
Sbjct: 434 EPTRGIDVGAKFDIYGLLAELARQGKALVVVSSDLRELMLICDRIAVLSAGRLIDTFARD 493

Query: 485 QADERQALSLA 495
              + Q L+ A
Sbjct: 494 HWSQDQLLAAA 504



 Score = 85.1 bits (209), Expect = 5e-21
 Identities = 60/229 (26%), Positives = 109/229 (47%), Gaps = 14/229 (6%)

Query: 25  DISFDCYAGQVHALMGENGAGKSTLLKILSGNYAPTTGSVVING--QEMSFSDTTAALNA 82
           ++SF+  AG++  + G  GAG++ LL+++ G     +G + +    Q +S     AA+ A
Sbjct: 282 EVSFEVRAGEIFGISGLIGAGRTELLRLIYGADRADSGGIALGQPPQAVSIDSPKAAVRA 341

Query: 83  GVAIIYQELH---LVPEMTVAENIYLGQLPHKGGIVNRSLLNYEAGLQLKHLGMDI---- 135
           G+A+I ++     L+   +++ NI LG L   G +    +L+ EA   L    +      
Sbjct: 342 GIALITEDRKGEGLLLTQSISANIALGNL---GAVSRAGVLDSEAEKALAERQIQAMRIR 398

Query: 136 --DPDTPLKYLSIGQWQMVEIAKALARNAKIIAFDEPTSSLSAREIDNLFRVIRELRKEG 193
                  +  LS G  Q V I + L R+ +++ FDEPT  +      +++ ++ EL ++G
Sbjct: 399 SAGAQQVVGELSGGNQQKVVIGRWLERDCQVLLFDEPTRGIDVGAKFDIYGLLAELARQG 458

Query: 194 RVILYVSHRMEEIFALSDAITVFKDGRYVKTFTDMQQVDHDALVQAMVG 242
           + ++ VS  + E+  + D I V   GR + TF          L  A  G
Sbjct: 459 KALVVVSSDLRELMLICDRIAVLSAGRLIDTFARDHWSQDQLLAAAFAG 507


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: 686
Number of extensions: 28
Number of successful extensions: 9
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: 524
Length adjustment: 35
Effective length of query: 469
Effective length of database: 489
Effective search space:   229341
Effective search space used:   229341
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