GapMind for catabolism of small carbon sources

 

Aligments for a candidate for araVsh in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter related (characterized, see rationale)
to candidate Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= uniprot:A0KWY5
         (499 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410 L-arabinose transport
           ATP-binding protein AraG (TC 3.A.1.2.2)
          Length = 514

 Score =  325 bits (832), Expect = 3e-93
 Identities = 184/492 (37%), Positives = 304/492 (61%), Gaps = 8/492 (1%)

Query: 5   LELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFL 64
           L    I K +PGVKAL+ +S     G+VHAL+GENGAGKSTL+K++ GA +   GD+   
Sbjct: 16  LRFNGIGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPSSGDLQIG 75

Query: 65  GEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARAV 124
            + + F +  D+  +G++ ++QE++LVP +TVA+NLFLG+ P   GLI+   +   A A 
Sbjct: 76  EQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPASFGLINRGVLRQQALAC 135

Query: 125 LTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILN 184
           L     +ID    +   S+  +QL+ IA+ ++  A V+  DEPT+SL A+E+  L  I+ 
Sbjct: 136 LKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAIIG 195

Query: 185 QLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYL-TAELPQPKLIEAMLGRSLQE 243
           +L+ +G  +++++H +++V++I + +TV ++G+F+  +   + L   +L+  M+GR +Q+
Sbjct: 196 RLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALTHDQLVTCMVGRDIQD 255

Query: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303
            + D + + R      AV L ++ +   G  + ++    KG+ +GL GL+G+GR+E+   
Sbjct: 256 -IYDYRSRPR-----GAVALKVDGLLGPGLREPVSFEAHKGEILGLFGLVGAGRTELFRM 309

Query: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENI-ILALQ 362
           + GL    +G + L G++L L  P DAI+AGI LCPEDRK +GI+   S+ ENI I A  
Sbjct: 310 LSGLTRNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARG 369

Query: 363 ARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILL 422
           A   +   L    +++ A   I  L++ TP+A + I  LSGGNQQK IL RWL++   +L
Sbjct: 370 AHSTFGCLLRGLWEKDNADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVL 429

Query: 423 VLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVREL 482
           +LDEPTRGIDIGA AEI ++I  L   G++++V SS+L E++  S++++VL +     EL
Sbjct: 430 LLDEPTRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGEL 489

Query: 483 SGAELTSQHVMQ 494
           +  +    +++Q
Sbjct: 490 TREQANESNLLQ 501



 Score = 80.9 bits (198), Expect = 1e-19
 Identities = 66/235 (28%), Positives = 112/235 (47%), Gaps = 15/235 (6%)

Query: 15  PGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPM 74
           PG++  E VS     GE+  L G  GAG++ L ++++G      G +   G     ++P 
Sbjct: 277 PGLR--EPVSFEAHKGEILGLFGLVGAGRTELFRMLSGLTRNTAGRLELRGRELKLHSPR 334

Query: 75  DAQKAGISTVYQE---VNLVPNLTVAQNLFLGYEPRRL-------GLIHFKKMYADARAV 124
           DA  AGI    ++     ++P  +VA+N+ +              GL  ++K  AD +  
Sbjct: 335 DAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGL--WEKDNADKQIK 392

Query: 125 LTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILN 184
             + K   + +  +   S   QQ   + R ++M  KVL+LDEPT  +D      ++ I++
Sbjct: 393 ALKVKTP-NAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIH 451

Query: 185 QLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGR 239
            L A G+A++ ++  L +V  ISDRI VL  G   GE    +  +  L++  L R
Sbjct: 452 NLAASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELTREQANESNLLQLALPR 506


Lambda     K      H
   0.319    0.136    0.377 

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: 578
Number of extensions: 31
Number of successful extensions: 7
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: 499
Length of database: 514
Length adjustment: 34
Effective length of query: 465
Effective length of database: 480
Effective search space:   223200
Effective search space used:   223200
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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