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 GFF2332 PS417_11890 D-ribose transporter ATP-binding protein

Query= uniprot:D8J111
         (520 letters)



>lcl|FitnessBrowser__WCS417:GFF2332 PS417_11890 D-ribose transporter
           ATP-binding protein
          Length = 517

 Score =  469 bits (1206), Expect = e-136
 Identities = 251/492 (51%), Positives = 340/492 (69%), Gaps = 4/492 (0%)

Query: 22  VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILL 81
           ++ + N+ K FPGV+AL + Q  +  G V ALMGENGAGKSTLMKI++G+YQ D+G+I L
Sbjct: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82

Query: 82  DGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNRQA 141
            GKP+    P  AQ  GI +IHQELNLM H+S A+NI+IGRE   ++ + ++  E++R  
Sbjct: 83  RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHM-VNHREMHRCT 141

Query: 142 AAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFR 201
           A + AR+R+++DP   VG L++A +QMVEIAKA+S+DS +LIMDEPT+A+   E+A LF 
Sbjct: 142 AELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201

Query: 202 IIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVGRAL 261
           II DL++QG GIVYI+HKM+E+  IAD V+V RDG YI        + D++ISMMVGR L
Sbjct: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261

Query: 262 DGEQRIP-PDTSRNDVVLEVRGLNRGRAIRDVSFTLRKGEILGFAGLMGAGRTEVARAIF 320
              Q  P  +T   D++L VR L      +DVSF L  GEILG AGLMG+GRT VA  IF
Sbjct: 262 S--QLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIF 319

Query: 321 GADPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRF 380
           G  P  +G+I + G    I  P  A+  G   L+EDRK  GL   + V  N+ ++ +  +
Sbjct: 320 GITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 379

Query: 381 TRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFD 440
           T  GF+ Q+A+R   +   ++L +KTPS+EQ    LSGGNQQK ++A+WL+ +  +L  D
Sbjct: 380 TGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILD 439

Query: 441 EPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARA 500
           EPTRGIDVGAK+EIY+L+  LA +G A++MISSELPEVL MS RV+VM EG + G L R+
Sbjct: 440 EPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRS 499

Query: 501 DATQEKIMQLAT 512
           +ATQEK+MQLA+
Sbjct: 500 EATQEKVMQLAS 511



 Score =  100 bits (250), Expect = 1e-25
 Identities = 62/221 (28%), Positives = 117/221 (52%), Gaps = 6/221 (2%)

Query: 43  FELAAGEVHALMGENGAGKSTLMKILSGVYQRDSGDILLDGKPVEITEPRQAQALGIGII 102
           F+L AGE+  + G  G+G++ + + + G+    SG I LDGK V I++P  A   G  ++
Sbjct: 293 FDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIEKGFALL 352

Query: 103 HQELNLMNH---LSAAQNIFIGREPRKAMGLFIDEDELNRQAAAIFARMRLDMDPSTP-- 157
            ++  L      LS  +N+ +   P      FI +  L      +  ++R+   PS    
Sbjct: 353 TEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKT-PSLEQC 411

Query: 158 VGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAELFRIIRDLQAQGVGIVYIS 217
           +  L+   QQ   +A+ L  + R+LI+DEPT  ++    AE++R+I  L ++G+ ++ IS
Sbjct: 412 IDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMIS 471

Query: 218 HKMDELRQIADRVSVMRDGKYIATVPMQETSMDTIISMMVG 258
            ++ E+  ++DRV VM +G+ + T+   E + + ++ +  G
Sbjct: 472 SELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512



 Score = 89.0 bits (219), Expect = 4e-22
 Identities = 70/254 (27%), Positives = 119/254 (46%), Gaps = 11/254 (4%)

Query: 267 IPPDTSRNDVVLEVRGLNRGR----AIRDVSFTLRKGEILGFAGLMGAGRTEVARAIFGA 322
           + P T     +LE+  +++G     A+ DV   +R G +L   G  GAG++ + + I G 
Sbjct: 13  LQPQTLEEPYLLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGI 72

Query: 323 DPLEAGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMDVQANIALSSMGRFTR 382
              +AGEI + G   V ++P  A   GI  + ++     L   M +  NI +    +   
Sbjct: 73  YQPDAGEIRLRGKPIVFETPLAAQKAGIAMIHQE---LNLMPHMSIAENIWIGRE-QLNS 128

Query: 383 VGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIAKWLLRDCDILFFDEP 442
           +  ++ R +       + +L I     E+Q   LS   +Q + IAK +  D DIL  DEP
Sbjct: 129 LHMVNHREMHRCTAELLARLRINLDP-EEQVGNLSIAERQMVEIAKAVSYDSDILIMDEP 187

Query: 443 TRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLVMCEGRITGELARADA 502
           T  I     + ++ ++  L  QGK IV I+ ++ EV  ++  V V  +G   G L RAD+
Sbjct: 188 TSAITEKEVAHLFSIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIG-LQRADS 246

Query: 503 -TQEKIMQLATQRE 515
              + ++ +   RE
Sbjct: 247 MNSDSLISMMVGRE 260


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: 600
Number of extensions: 33
Number of successful extensions: 8
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 4
Number of HSP's successfully gapped: 3
Length of query: 520
Length of database: 517
Length adjustment: 35
Effective length of query: 485
Effective length of database: 482
Effective search space:   233770
Effective search space used:   233770
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