Alignments for a candidate for araVsh in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for araVsh in Pseudomonas fluorescens GW456-L13

Align ABC transporter related (characterized, see rationale)
to candidate PfGW456L13_3911 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= uniprot:A0KWY5
         (499 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3911
          Length = 517

 Score =  294 bits (753), Expect = 4e-84
 Identities = 174/473 (36%), Positives = 277/473 (58%), Gaps = 10/473 (2%)

Query: 4   ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63
           +L +  I K Y     L  + L L  GEV AL GENGAGKSTL K++ G  +   G + +
Sbjct: 9   VLSVSGIGKTY-AQPVLAGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQY 67

Query: 64  LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123
            G+     +   A+  GI  V QE+NL+P L+VA+NLFL   P + G I  K++   A  
Sbjct: 68  QGQDYRPGSRAQAEALGIRMVMQELNLLPTLSVAENLFLDNLPSKGGWISRKQLRKAAIE 127

Query: 124 VLTQFKLD-IDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGI 182
            +    LD ID    + +  I  QQ++ IAR +     VL+LDEPTA L A+EV++LF  
Sbjct: 128 AMAHVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQ 187

Query: 183 LNQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQ 242
           + +L+++GV+I++I+H L+++ +++ RI VLR+G  +     A     +L+  M+GR L 
Sbjct: 188 ITRLQSRGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGRELG 247

Query: 243 EQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302
           E +      +    +  A +L++  +S    ++ ++  V  G+  G++GL+G+GR+E+  
Sbjct: 248 EHI------DMGARKIGAPVLTVNGLSRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLR 301

Query: 303 AVFGLDLVDSGSIHLAG--QKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILA 360
            +FG D+ DSG+I L    Q +N+  PVDA+  GIAL  EDRK +G++   SI  NI L 
Sbjct: 302 LIFGADIADSGTIALGAPAQVINVRSPVDAVGHGIALITEDRKGEGLLLTQSIGANIALG 361

Query: 361 LQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPI 420
               I    ++ N +++ +AQ  ID ++I +    + + +LSGGNQQKV++ RWL  +  
Sbjct: 362 NMPGISGAGFVDNDKERALAQRQIDAMRIRSSGPAQLVSELSGGNQQKVVIGRWLERDCS 421

Query: 421 LLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473
           +L+ DEPTRGID+GA  +I  L+  L  +G +L+V SS+L EL+   +++ VL
Sbjct: 422 VLLFDEPTRGIDVGAKFDIYNLLGELTRQGKALVVVSSDLRELMLICDRIGVL 474



 Score = 79.3 bits (194), Expect = 3e-19
 Identities = 66/227 (29%), Positives = 109/227 (48%), Gaps = 14/227 (6%)

Query: 20  LEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFN--TPMDAQ 77
           + DVS  + AGE+  + G  GAG++ L++++ GA   D G I      Q  N  +P+DA 
Sbjct: 273 VRDVSFEVRAGEIFGISGLIGAGRTELLRLIFGADIADSGTIALGAPAQVINVRSPVDAV 332

Query: 78  KAGISTVYQE---VNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARAVLTQFKLD--- 131
             GI+ + ++     L+   ++  N+ LG  P   G+     +  D    L Q ++D   
Sbjct: 333 GHGIALITEDRKGEGLLLTQSIGANIALGNMP---GISGAGFVDNDKERALAQRQIDAMR 389

Query: 132 IDVSAP---LSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKA 188
           I  S P   +S+ S   QQ + I R +     VL+ DEPT  +D      ++ +L +L  
Sbjct: 390 IRSSGPAQLVSELSGGNQQKVVIGRWLERDCSVLLFDEPTRGIDVGAKFDIYNLLGELTR 449

Query: 189 KGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEA 235
           +G A+V ++  L ++  I DRI VL  G  I  +      Q +L+ A
Sbjct: 450 QGKALVVVSSDLRELMLICDRIGVLSAGSLIDTFDRDSWTQDELLAA 496



 Score = 72.0 bits (175), Expect = 5e-17
 Identities = 54/203 (26%), Positives = 101/203 (49%), Gaps = 7/203 (3%)

Query: 274 IQSMNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISA 333
           +  ++LT+ +G+ + L G  G+G+S +   + GL    +G +   GQ         A + 
Sbjct: 24  LAGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQYQGQDYRPGSRAQAEAL 83

Query: 334 GIALCPEDRKIDGIIGPLSIRENIILA-LQARIGWWRYLSNTRQQEIAQFFIDKLQIATP 392
           GI +  ++  +   +  LS+ EN+ L  L ++ GW   +S  + ++ A   +  + +   
Sbjct: 84  GIRMVMQELNL---LPTLSVAENLFLDNLPSKGGW---ISRKQLRKAAIEAMAHVGLDAI 137

Query: 393 DADKPIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMS 452
           D D  + +L  G+QQ V +AR L  +  +L+LDEPT  +       + + I  L   G+S
Sbjct: 138 DPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQSRGVS 197

Query: 453 LLVASSELDELVAFSNKVVVLRD 475
           ++  S  L+EL   + ++ VLRD
Sbjct: 198 IIYISHRLEELARVAQRIAVLRD 220


Lambda     K      H
   0.319    0.136    0.377 

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: 590
Number of extensions: 25
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 3
Length of query: 499
Length of database: 517
Length adjustment: 34
Effective length of query: 465
Effective length of database: 483
Effective search space:   224595
Effective search space used:   224595
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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Steps (tab-delimited)
Rules (tab-delimited)
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