GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS05250 in Pseudomonas fluorescens FW300-N1B4

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate Pf1N1B4_410 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= uniprot:D8J111
         (520 letters)



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

 Score =  348 bits (893), Expect = e-100
 Identities = 203/499 (40%), Positives = 304/499 (60%), Gaps = 13/499 (2%)

Query: 23  IALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLD 82
           +    + K FPGV ALD   F    G+VHALMGENGAGKSTL+KIL G Y   SGD+ + 
Sbjct: 16  LRFNGIGKTFPGVKALDGISFVAHPGQVHALMGENGAGKSTLLKILGGAYTPSSGDLQIG 75

Query: 83  GKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQAA 142
            +         +   G+ +IHQEL+L+  ++ A+N+F+G  P  + GL I+   L +QA 
Sbjct: 76  EQKRIFKSTADSIGSGVAVIHQELHLVPEMTVAENLFLGHLPA-SFGL-INRGVLRQQAL 133

Query: 143 AIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRI 202
           A    +  ++DP   VG L++ ++Q+VEIAKALS  + V+  DEPT++L+  EI  L  I
Sbjct: 134 ACLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAI 193

Query: 203 IRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVP-MQETSMDTIISMMVGRAL 261
           I  L+ +G  ++Y+SH+M+E+ +I + V+V +DG+++ T   M   + D +++ MVGR +
Sbjct: 194 IGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRFVRTFEDMSALTHDQLVTCMVGRDI 253

Query: 262 DG--EQRIPPDTSRNDVVLEVRGLNRGRAIRD-VSFTLRKGEILGFAGLMGAGRTEVARA 318
               + R  P   R  V L+V GL  G  +R+ VSF   KGEILG  GL+GAGRTE+ R 
Sbjct: 254 QDIYDYRSRP---RGAVALKVDGL-LGPGLREPVSFEAHKGEILGLFGLVGAGRTELFRM 309

Query: 319 IFGADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMG 378
           + G     AG + + G +  + SP DA+A GI    EDRK  G+     V  NI +S+ G
Sbjct: 310 LSGLTRNTAGRLELRGRELKLHSPRDAIAAGILLCPEDRKKEGILPLASVAENINISARG 369

Query: 379 RFTRVGFMDQRAI--REAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDI 436
             +  G +  R +  ++ A   ++ L +KTP+  Q+   LSGGNQQK ++ +WL     +
Sbjct: 370 AHSTFGCL-LRGLWEKDNADKQIKALKVKTPNAAQKIMYLSGGNQQKAILGRWLSMPMKV 428

Query: 437 LFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGE 496
           L  DEPTRGID+GAK+EIY+++  LA  G A++++SS+L EV+ +S R+LV+CEG + GE
Sbjct: 429 LLLDEPTRGIDIGAKAEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVLCEGAMRGE 488

Query: 497 LARADATQEKIMQLATQRE 515
           L R  A +  ++QLA  R+
Sbjct: 489 LTREQANESNLLQLALPRQ 507


Lambda     K      H
   0.320    0.135    0.372 

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: 628
Number of extensions: 29
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 520
Length of database: 514
Length adjustment: 35
Effective length of query: 485
Effective length of database: 479
Effective search space:   232315
Effective search space used:   232315
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