GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS05250 in Pseudomonas simiae WCS417

Align Ribose import ATP-binding protein RbsA; EC 7.5.2.7 (characterized, see rationale)
to candidate GFF2366 PS417_12065 D-ribose transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>lcl|FitnessBrowser__WCS417:GFF2366 PS417_12065 D-ribose transporter
           ATP-binding protein
          Length = 495

 Score =  369 bits (946), Expect = e-106
 Identities = 205/492 (41%), Positives = 302/492 (61%), Gaps = 3/492 (0%)

Query: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81
           ++   +V K + GV AL + +  L AG VHAL G NGAGKST + IL G+ QRD+G ILL
Sbjct: 6   LLQAEHVAKAYAGVPALRDGRLSLRAGSVHALCGGNGAGKSTFLSILMGITQRDAGSILL 65

Query: 82  DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141
           +G PV+   P +A A GI +I QEL  + +++ A+NI++GREPR+A G  +D   LNR+ 
Sbjct: 66  NGAPVQFNRPSEALAAGIAMITQELEPIPYMTVAENIWLGREPRRA-GCIVDNKALNRRT 124

Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201
             +   +  D+D ++P+  L+VA+ Q+VEIAKA S D +V+IMDEPT+A+   E   LF+
Sbjct: 125 RELLDSLEFDVDATSPMHRLSVAQIQLVEIAKAFSHDCQVMIMDEPTSAIGEHEAQTLFK 184

Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261
            IR L AQG GIVY+SH++ EL QIAD  S+ RDG ++ +  M +   D ++  +VG+ L
Sbjct: 185 AIRRLTAQGAGIVYVSHRLSELAQIADDYSIFRDGAFVESGRMADIDRDHLVRGIVGQEL 244

Query: 262 DG-EQRIPPDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIF 320
              + ++  + + N   L+V  L+R     D+S  LR+GEILG  GLMG+GR+E    I+
Sbjct: 245 TRIDHKVGRECAAN-TCLQVDNLSRAGEFHDISLQLRQGEILGIYGLMGSGRSEFLNCIY 303

Query: 321 GADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRF 380
           G    ++G + + G    I  P   +  G+  ++EDRK  GL +   + +NIALS+  R 
Sbjct: 304 GLTVADSGSVTLQGKPMPIGLPKATINAGMSLVTEDRKDSGLVLTGSILSNIALSAYKRL 363

Query: 381 TRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFD 440
           +    ++ R   + A+  V++L IKT S+E     +SGGNQQK+V+AK L  +   L  D
Sbjct: 364 SSWSLINARKETQLAEDMVKRLQIKTTSLELPVASMSGGNQQKVVLAKCLSTEPVCLLCD 423

Query: 441 EPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARA 500
           EPTRGID GAK EIY LLD     G A +++SSE PE+L +S R+ V   GR+       
Sbjct: 424 EPTRGIDEGAKQEIYHLLDQFVRGGGAAIVVSSEAPELLHLSDRIAVFKGGRLVTISTDT 483

Query: 501 DATQEKIMQLAT 512
             +QE +++LA+
Sbjct: 484 ALSQEALLRLAS 495


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: 566
Number of extensions: 27
Number of successful extensions: 7
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: 495
Length adjustment: 34
Effective length of query: 486
Effective length of database: 461
Effective search space:   224046
Effective search space used:   224046
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