GapMind for catabolism of small carbon sources

 

Aligments for a candidate for BPHYT_RS16930 in Pseudomonas simiae WCS417

Align Arabinose import ATP-binding protein AraG; EC 7.5.2.12 (characterized, see rationale)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein

Query= uniprot:A0A165ZSX8
         (514 letters)



>lcl|FitnessBrowser__WCS417:GFF2332 PS417_11890 D-ribose transporter
           ATP-binding protein
          Length = 517

 Score =  396 bits (1018), Expect = e-115
 Identities = 208/489 (42%), Positives = 315/489 (64%), Gaps = 3/489 (0%)

Query: 16  LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQIG 75
           L    I K FPGV ALA++     PG V ALMGENGAGKSTL+KI+ G Y P +G++++ 
Sbjct: 24  LEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLR 83

Query: 76  EQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGHLPAR-FGLVNRGVLRQQALT 134
            + + F+    +  +G+A+IHQEL+L+P M++AEN+++G        +VN   + +    
Sbjct: 84  GKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAE 143

Query: 135 LLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194
           LL  L   +DP+E+VG LS+ +RQ+VEIAKA+S  + ++  DEPTS+++ +E+  L +II
Sbjct: 144 LLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSII 203

Query: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDIQ 254
             L+ +GK ++Y++H+M EVF I + V VF+DG Y+   +    +  D L++ MVGR++ 
Sbjct: 204 ADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIG-LQRADSMNSDSLISMMVGRELS 262

Query: 255 DIYDYRPRERGDVALQVKGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLE 314
            ++  R    GD+ L V+ L   G+ + VSF +H GEILG+ GL+G+GRT +   + G+ 
Sbjct: 263 QLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGIT 322

Query: 315 RQREGSLVLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTL 374
               G + L  K +++  P  AI  G  L  EDRK  G+ P  SV EN+ ++  P H T 
Sbjct: 323 PSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLP-HYTG 381

Query: 375 GCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEP 434
              ++    R   +   K L+VKTP+  Q I  LSGGNQQKA+L RWL    ++L+LDEP
Sbjct: 382 NGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEP 441

Query: 435 TRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQA 494
           TRGID+GAKAEIY++I  LA++G+AVI++SS+L EV+G+SDR++V+ EG + G L R +A
Sbjct: 442 TRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEA 501

Query: 495 NESNLLQLA 503
            +  ++QLA
Sbjct: 502 TQEKVMQLA 510



 Score = 79.3 bits (194), Expect = 3e-19
 Identities = 59/236 (25%), Positives = 113/236 (47%), Gaps = 6/236 (2%)

Query: 272 KGLLGPGLHEPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLERQREGSLVLHDKELKLR 331
           KG  G      V  +V  G +L L G  GAG++ L+++++G+ +   G + L  K +   
Sbjct: 31  KGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFE 90

Query: 332 SPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTLGCLLRGDWERGNADKQI 391
           +P  A  AG+ +  ++     ++P  S+ ENI I  R   ++L  +   +  R  A+  +
Sbjct: 91  TPLAAQKAGIAMIHQELN---LMPHMSIAENIWIG-REQLNSLHMVNHREMHRCTAEL-L 145

Query: 392 KSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIH 451
             L++      Q +  LS   +Q   + + +S    +L++DEPT  I     A ++ II 
Sbjct: 146 ARLRINLDPEEQ-VGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIA 204

Query: 452 NLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPRQ 507
           +L + G  ++ ++  + EV  I+D + V  +G   G    D  N  +L+ + + R+
Sbjct: 205 DLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRE 260


Lambda     K      H
   0.320    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: 665
Number of extensions: 30
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 514
Length of database: 517
Length adjustment: 35
Effective length of query: 479
Effective length of database: 482
Effective search space:   230878
Effective search space used:   230878
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