GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rbsA in Pseudomonas fluorescens FW300-N1B4

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_410
          Length = 514

 Score =  409 bits (1051), Expect = e-118
 Identities = 223/490 (45%), Positives = 320/490 (65%), Gaps = 3/490 (0%)

Query: 5   LQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWL 64
           L+  GI K FPGVKAL G +   +PG+V AL+GENGAGKST++K+L G YT  +G L   
Sbjct: 16  LRFNGIGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPSSGDLQIG 75

Query: 65  GKETTFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEADK 124
            ++  F     S  +G+ +IHQEL+L+P++T+AEN+FLG      FG I+   +  +A  
Sbjct: 76  EQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGH-LPASFGLINRGVLRQQALA 134

Query: 125 LLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVI 184
            L  L       + VG LS+G +Q+VEIAK LS  + VI  DEPT +L+  E + L  +I
Sbjct: 135 CLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 194

Query: 185 RELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAERE-VASLTEDSLIEMMVGRKLE 243
             L+ +G+ ++Y+SHRM+E+F IC+ VTVF+DG+F+   E +++LT D L+  MVGR ++
Sbjct: 195 GRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALTHDQLVTCMVGRDIQ 254

Query: 244 DQYPHLDKAPGDIRLKVDNLCGPGVND-VSFTLRKGEILGVSGLMGAGRTELMKVLYGAL 302
           D Y +  +  G + LKVD L GPG+ + VSF   KGEILG+ GL+GAGRTEL ++L G  
Sbjct: 255 DIYDYRSRPRGAVALKVDGLLGPGLREPVSFEAHKGEILGLFGLVGAGRTELFRMLSGLT 314

Query: 303 PRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSRA 362
             T+G + L G E+   SP+D +A GI+   EDRK++G++   SV EN++++A    S  
Sbjct: 315 RNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTF 374

Query: 363 GGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDEP 422
           G  L+   E+      I+   VKTP+  Q I  LSGGNQQK  + R L    KVL+LDEP
Sbjct: 375 GCLLRGLWEKDNADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEP 434

Query: 423 TRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQA 482
           TRG+D+GAK EIYQ+I+   A G+++I+VSS++ EV+G+SDRI+V+ EG + GE TREQA
Sbjct: 435 TRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELTREQA 494

Query: 483 TQEVLMAAAV 492
            +  L+  A+
Sbjct: 495 NESNLLQLAL 504



 Score = 79.0 bits (193), Expect = 4e-19
 Identities = 57/234 (24%), Positives = 114/234 (48%), Gaps = 10/234 (4%)

Query: 15  PGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWLGKETTFTGPK 74
           PG++     +   + G ++ L G  GAG++ + ++L+G+    AG L   G+E     P+
Sbjct: 277 PGLR--EPVSFEAHKGEILGLFGLVGAGRTELFRMLSGLTRNTAGRLELRGRELKLHSPR 334

Query: 75  SSQEAGIGIIHQELN---LIPQLTIAENIFLG-REFVNRFGKID---WKTMYAEADKLLA 127
            +  AGI +  ++     ++P  ++AENI +  R   + FG +    W+   A+      
Sbjct: 335 DAIAAGILLCPEDRKKEGILPLASVAENINISARGAHSTFGCLLRGLWEKDNADKQIKAL 394

Query: 128 KLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRVIREL 187
           K+     + K++  LS G+QQ   + + LS   KV+++DEPT  +       ++++I  L
Sbjct: 395 KVKTPNAAQKIMY-LSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQIIHNL 453

Query: 188 KSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRK 241
            + G  ++ +S  + E+  I D + V  +G    E       E +L+++ + R+
Sbjct: 454 AASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELTREQANESNLLQLALPRQ 507


Lambda     K      H
   0.318    0.137    0.380 

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: 696
Number of extensions: 40
Number of successful extensions: 8
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: 501
Length of database: 514
Length adjustment: 34
Effective length of query: 467
Effective length of database: 480
Effective search space:   224160
Effective search space used:   224160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 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:

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