GapMind for catabolism of small carbon sources

 

Aligments for a candidate for PS417_11890 in Pseudomonas fluorescens GW456-L13

Align Inositol transport system ATP-binding protein (characterized)
to candidate PfGW456L13_2121 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= reanno::WCS417:GFF2332
         (517 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2121 L-arabinose
           transport ATP-binding protein AraG (TC 3.A.1.2.2)
          Length = 514

 Score =  390 bits (1003), Expect = e-113
 Identities = 210/493 (42%), Positives = 316/493 (64%), Gaps = 11/493 (2%)

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

Query: 84  GKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAE 143
            + + F++   +  +G+A+IHQEL+L+P M++AEN+++G     S  ++N   + +    
Sbjct: 76  ERTMDFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPA-SFGLINRSTLRQQALA 134

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

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

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

Query: 323 PSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGN 382
             S+GQ+ L G  +++  P  AI  G  L  EDRK  G+ P  SV EN+ ++    ++  
Sbjct: 315 RHSAGQLKLRGHELKLRSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTF 374

Query: 383 GFIQQKALRAL-----CEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLI 437
           G +    LR L      E   K L+VKTP+  Q I  LSGGNQQKA+L RWL    ++L+
Sbjct: 375 GCL----LRGLWEKDNAEQQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLL 430

Query: 438 LDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLD 497
           LDEPTRGID+GAKAEIY++I  LA+EG+AVI++SS+L EV+G+SDR++V+ EG L G L 
Sbjct: 431 LDEPTRGIDIGAKAEIYQIIHNLAAEGIAVIVVSSDLMEVMGISDRILVLCEGALRGELS 490

Query: 498 RSEATQEKVMQLA 510
           R +A +  ++QLA
Sbjct: 491 REQANESNLLQLA 503



 Score = 86.3 bits (212), Expect = 2e-21
 Identities = 57/225 (25%), Positives = 111/225 (49%), Gaps = 6/225 (2%)

Query: 42  VQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKAGIA 101
           V   V  G +L L G  GAG++ L+++++G+ +  AG+++LRG  +   +P  A  AGI 
Sbjct: 283 VSFEVHKGEILGLFGLVGAGRTELLRLLSGLARHSAGQLKLRGHELKLRSPRDAIAAGIL 342

Query: 102 MIHQELN---LMPHMSIAENIWIGREQLNSLHMVNHR---EMHRCTAELLARLRINLDPE 155
           +  ++     ++P  S+AENI I     +S      R   E      ++ A      +  
Sbjct: 343 LCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNAEQQIKALKVKTPNAA 402

Query: 156 EQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGIVY 215
           +++  LS   +Q   + + +S    +L++DEPT  I     A ++ II +L ++G  ++ 
Sbjct: 403 QKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNLAAEGIAVIV 462

Query: 216 ITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGRE 260
           ++  + EV  I+D + V  +G   G    +  N  +L+ + + R+
Sbjct: 463 VSSDLMEVMGISDRILVLCEGALRGELSREQANESNLLQLALPRQ 507


Lambda     K      H
   0.320    0.136    0.381 

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: 643
Number of extensions: 34
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: 517
Length of database: 514
Length adjustment: 35
Effective length of query: 482
Effective length of database: 479
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, 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