Alignments for a candidate for rbsA in Pseudomonas fluorescens FW300-N2E2

GapMind for catabolism of small carbon sources

Alignments for a candidate for rbsA in Pseudomonas fluorescens FW300-N2E2

Align ribose transport, ATP-binding protein RbsA; EC 3.6.3.17 (characterized)
to candidate Pf6N2E2_5969 L-arabinose transport ATP-binding protein AraG (TC 3.A.1.2.2)

Query= CharProtDB::CH_003578
         (501 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5969
          Length = 514

 Score =  403 bits (1036), Expect = e-117
 Identities = 219/491 (44%), Positives = 328/491 (66%), 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 IGRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYVRTFENMSELTHDQLVTCMVGRDI 253

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

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

Query: 362 AGGSLKHADEQQAVSDFIRLFNVKTPSMEQAIGLLSGGNQQKVAIARGLMTRPKVLILDE 421
            G  L+   E+      I+   VKTP+  Q I  LSGGNQQK  + R L    KVL+LDE
Sbjct: 374 LGCLLRGDWERGNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDE 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 = 82.4 bits (202), Expect = 3e-20
 Identities = 61/248 (24%), Positives = 124/248 (50%), Gaps = 14/248 (5%)

Query: 2   EALLQLKGIDKAFPGVKALSGAALNVYPGRVMALVGENGAGKSTMMKVLTGIYTRDAGTL 61
           +  LQ+KG+    PG+      +  V+ G ++ L G  GAG++ ++++L+G+  +  G+L
Sbjct: 266 DVALQVKGL--LGPGLH--EPVSFQVHKGEILGLFGLVGAGRTELLRLLSGLERQREGSL 321

Query: 62  LWLGKETTFTGPKSSQEAGIGIIHQELN---LIPQLTIAENIFLG-REFVNRFGKI---D 114
           +   KE     P+ +  AG+ +  ++     +IP  ++ ENI +  R   +  G +   D
Sbjct: 322 VLHDKELKLRSPRDAIAAGVLLCPEDRKKEGIIPLGSVGENINISARPSHSTLGCLLRGD 381

Query: 115 WKTMYAEADKLLAKLNLRFKS-DKLVGDLSIGDQQMVEIAKVLSFESKVIIMDEPTDALT 173
           W+     ADK +  L ++  +  + +  LS G+QQ   + + LS   KV+++DEPT  + 
Sbjct: 382 WER--GNADKQIKSLKVKTPTAGQKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGID 439

Query: 174 DTETESLFRVIRELKSQGRGIVYISHRMKEIFEICDDVTVFRDGQFIAEREVASLTEDSL 233
                 ++++I  L + G  ++ +S  + E+  I D + V  +G    E       E +L
Sbjct: 440 IGAKAEIYQIIHNLAADGIAVIVVSSDLMEVMGISDRILVLCEGAMRGELSRDQANESNL 499

Query: 234 IEMMVGRK 241
           +++ + R+
Sbjct: 500 LQLALPRQ 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: 682
Number of extensions: 29
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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Protein sequences (fasta format)
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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:

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