Alignments for a candidate for rbsA in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Pseudomonas simiae WCS417

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate GFF4164 PS417_21330 L-arabinose transporter ATP-binding protein

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__WCS417:GFF4164
          Length = 499

 Score =  407 bits (1046), Expect = e-118
 Identities = 221/493 (44%), Positives = 323/493 (65%), Gaps = 5/493 (1%)

Query: 3   ALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTLL 62
           A L+  GI K FPGVKALS  +    P  V AL+GENGAGKST++K+L G Y   +GTL 
Sbjct: 4   AALRFNGIGKEFPGVKALSQISFEARPREVHALMGENGAGKSTLLKILGGAYLPSSGTLQ 63

Query: 63  WLGKETT-FTGPKSSQEAGIGIIHQELNLIPQLTIAENIFLGREFVNRFGKIDWKTMYAE 121
            +G++T  F     S   G+ +IHQEL+L+P++T+AEN+FLG     RFG ++   +  +
Sbjct: 64  -IGEQTMDFKSAADSIACGVAVIHQELHLVPEMTVAENLFLGH-LPTRFGVVNRSQLRKQ 121

Query: 122 ADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTDTETESLF 181
           A   L  L      D+ +G LS+G +Q+VEIAK LS  + VI  DEPT +L+  E + L 
Sbjct: 122 ALACLKGLADEIDPDEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLM 181

Query: 182 RVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAE-REVASLTEDSLIEMMVGR 240
            +I  L+ +G+ ++Y+SHRM+E+F IC+ VTVF+DG+++    ++ +L+ D L+  MVGR
Sbjct: 182 AIITRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFDDMNALSHDQLVTCMVGR 241

Query: 241 KLEDQYPHLDKAPGDIRLKVDNLCGPGVND-VSFTLRKGEILGVSGLMGAGRTELMKVLY 299
            ++D Y +  +  G++ LKV+ L GPG+ + VS  + KGEILG+ GL+GAGRTEL ++L 
Sbjct: 242 DIQDIYDYRQREQGEVALKVEGLLGPGLREPVSLNVHKGEILGLFGLVGAGRTELFRLLS 301

Query: 300 GALPRTSGYVTLDGHEVVTRSPQDGLANGIVYISEDRKRDGLVLGMSVKENMSLTALRYF 359
           G    T+G + L G  +  RSP+D +A G++   EDRK++G++   SV EN++++A    
Sbjct: 302 GLTRSTAGSLALCGQTLQLRSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGAH 361

Query: 360 SRAGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLIL 419
           S  G  L+   E       I+   VKTP+ EQ I  LSGGNQQK  + R L    KVL+L
Sbjct: 362 STFGWLLRDGWETTNADRQIKAMKVKTPNAEQKIMYLSGGNQQKAILGRWLSMPMKVLLL 421

Query: 420 DEPTRGVDVGAKKEIYQLINQFKADGLSIILVSSEMPEVLGMSDRIIVMHEGHLSGEFTR 479
           DEPTRG+D+GAK EIYQ+I+   A G+++I+VSS++ EV+G+SDRI+VM EG L+GE TR
Sbjct: 422 DEPTRGIDIGAKSEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVMSEGALTGELTR 481

Query: 480 EQATQEVLMAAAV 492
           +QA +  L+  A+
Sbjct: 482 DQADEARLLQLAL 494



 Score = 87.4 bits (215), Expect = 1e-21
 Identities = 63/246 (25%), Positives = 122/246 (49%), Gaps = 12/246 (4%)

Query: 2   EALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTL 61
           E  L+++G+    PG++     +LNV+ G ++ L G  GAG++ + ++L+G+    AG+L
Sbjct: 256 EVALKVEGL--LGPGLR--EPVSLNVHKGEILGLFGLVGAGRTELFRLLSGLTRSTAGSL 311

Query: 62  LWLGKETTFTGPKSSQEAGIGIIHQELN---LIPQLTIAENIFLG-REFVNRFGKI---D 114
              G+      P+ +  AG+ +  ++     +IP  ++AENI +  R   + FG +    
Sbjct: 312 ALCGQTLQLRSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGAHSTFGWLLRDG 371

Query: 115 WKTMYAEADKLLAKLNLRFKSDKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALTD 174
           W+T  A+      K+       K++  LS G+QQ   + + LS   KV+++DEPT  +  
Sbjct: 372 WETTNADRQIKAMKVKTPNAEQKIMY-LSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDI 430

Query: 175 TETESLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSLI 234
                ++++I  L + G  ++ +S  + E+  I D + V  +G    E       E  L+
Sbjct: 431 GAKSEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVMSEGALTGELTRDQADEARLL 490

Query: 235 EMMVGR 240
           ++ + R
Sbjct: 491 QLALPR 496


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: 646
Number of extensions: 31
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: 499
Length adjustment: 34
Effective length of query: 467
Effective length of database: 465
Effective search space:   217155
Effective search space used:   217155
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources