GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rbsA in Pseudomonas fluorescens FW300-N2C3

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate AO356_20250 AO356_20250 L-arabinose transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_20250 AO356_20250
           L-arabinose transporter ATP-binding protein
          Length = 514

 Score =  407 bits (1046), Expect = e-118
 Identities = 220/491 (44%), Positives = 329/491 (67%), Gaps = 5/491 (1%)

Query: 5   LQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWL 64
           L+  GI K+FPGV+AL+  +   +PG+V AL+GENGAGKST++K+L G Y   +G L  +
Sbjct: 16  LRFNGIGKSFPGVQALANISFVAHPGQVHALMGENGAGKSTLLKILGGAYIPSSGDLQ-I 74

Query: 65  GKET-TFTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAEAD 123
           G++T  F G   S  +G+ +IHQEL+L+P++T+AEN+FLG     RFG ++   +  +A 
Sbjct: 75  GEQTMAFKGTADSIASGVAVIHQELHLVPEMTVAENLFLGH-LPARFGLVNRGVLRQQAL 133

Query: 124 KLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFRV 183
            LL  L       + VG LS+G +Q+VEIAK LS  + VI  DEPT +L+  E + L  +
Sbjct: 134 TLLKGLADEIDPQEKVGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAI 193

Query: 184 IRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAERE-VASLTEDSLIEMMVGRKL 242
           I  L+ +G+ ++Y+SHRM+E+F IC+ VTVF+DG+++   E ++ LT D L+  MVGR +
Sbjct: 194 IARLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDI 253

Query: 243 EDQYPHLDKAPGDIRLKVDNLCGPGVND-VSFTLRKGEILGVSGLMGAGRTELMKVLYGA 301
           +D Y +  +  GD+ L+V +L GPG+ + VSF + KGEILG+ GL+GAGRTEL ++L G 
Sbjct: 254 QDIYDYRPRERGDVALQVKSLLGPGLREPVSFQVHKGEILGLFGLVGAGRTELFRLLSGL 313

Query: 302 LPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYFSR 361
             ++ G + L G E+  RSP+D +A G++   EDRK++G++   SV EN++++A    S 
Sbjct: 314 ERQSEGSLVLHGKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPAHSA 373

Query: 362 AGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDE 421
            G  L+   E+      I+   VKTP+  Q I  LSGGNQQK  + R L    KVL+LDE
Sbjct: 374 LGCLLRGDWERGNADKQIKSLKVKTPAASQKIMYLSGGNQQKAILGRWLSMPMKVLLLDE 433

Query: 422 PTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTREQ 481
           PTRG+D+GAK EIYQ+I+   ADG+++I+VSS++ EV+G+SDRI+V+ EG + GE +R+Q
Sbjct: 434 PTRGIDIGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQ 493

Query: 482 ATQEVLMAAAV 492
           A +  L+  A+
Sbjct: 494 ANESNLLQLAL 504



 Score = 84.7 bits (208), Expect = 7e-21
 Identities = 61/239 (25%), Positives = 119/239 (49%), Gaps = 16/239 (6%)

Query: 17  VKALSGAALN------VYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLLWLGKETTF 70
           VK+L G  L       V+ G ++ L G  GAG++ + ++L+G+  +  G+L+  GKE   
Sbjct: 271 VKSLLGPGLREPVSFQVHKGEILGLFGLVGAGRTELFRLLSGLERQSEGSLVLHGKELKL 330

Query: 71  TGPKSSQEAGIGIIHQELN---LIPQLTIAENIFLG-REFVNRFGKI---DWKTMYAEAD 123
             P+ +  AG+ +  ++     +IP  ++ ENI +  R   +  G +   DW+     AD
Sbjct: 331 RSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPAHSALGCLLRGDWER--GNAD 388

Query: 124 KLLAKLNLRFKS-DKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLFR 182
           K +  L ++  +  + +  LS G+QQ   + + LS   KV+++DEPT  +       +++
Sbjct: 389 KQIKSLKVKTPAASQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKAEIYQ 448

Query: 183 VIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLIEMMVGRK 241
           +I  L + G  ++ +S  + E+  I D + V  +G    E       E +L+++ + R+
Sbjct: 449 IIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNLLQLALPRQ 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: 653
Number of extensions: 27
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 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