GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__WCS417:GFF2332
          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 (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