Alignments for a candidate for PS417_11890 in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Pseudomonas fluorescens GW456-L13

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

Query= reanno::WCS417:GFF2332
         (517 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3911
          Length = 517

 Score =  347 bits (889), Expect = e-100
 Identities = 191/491 (38%), Positives = 300/491 (61%), Gaps = 5/491 (1%)

Query: 23  LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRL 82
           +L +  I K +   V LA + L +  G VLAL GENGAGKSTL KII G+  P  G+++ 
Sbjct: 9   VLSVSGIGKTYAQPV-LAGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQY 67

Query: 83  RGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTA 142
           +G+     +   A+  GI M+ QELNL+P +S+AEN+++          ++ +++ +   
Sbjct: 68  QGQDYRPGSRAQAEALGIRMVMQELNLLPTLSVAENLFLDNLPSKG-GWISRKQLRKAAI 126

Query: 143 ELLARLRIN-LDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFS 201
           E +A + ++ +DP+  VG L I  +QMVEIA+ +  D  +LI+DEPT+ +T +EV  LF 
Sbjct: 127 EAMAHVGLDAIDPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFE 186

Query: 202 IIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGREL 261
            I  L+S+G  I+YI+H++ E+  +A  +AV RDG+ + ++   + NS+ L+++MVGREL
Sbjct: 187 QITRLQSRGVSIIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVGREL 246

Query: 262 SQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGI 321
            +   +    IG  +LTV  L+     +DVSF++ AGEI GI+GL+G+GRT +   IFG 
Sbjct: 247 GEHIDMGARKIGAPVLTVNGLSRSDKVRDVSFEVRAGEIFGISGLIGAGRTELLRLIFGA 306

Query: 322 TPSSSGQITLDGKA--VRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHY 379
             + SG I L   A  + +  P  A+  G AL+TEDRK  GL    S+  N+ +  +P  
Sbjct: 307 DIADSGTIALGAPAQVINVRSPVDAVGHGIALITEDRKGEGLLLTQSIGANIALGNMPGI 366

Query: 380 TGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILD 439
           +G GF+     RAL +     +R+++    Q +  LSGGNQQK ++ RWL  +  +L+ D
Sbjct: 367 SGAGFVDNDKERALAQRQIDAMRIRSSGPAQLVSELSGGNQQKVVIGRWLERDCSVLLFD 426

Query: 440 EPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRS 499
           EPTRGIDVGAK +IY L+  L  +G A++++SS+L E++ + DR+ V+  G L+ T DR 
Sbjct: 427 EPTRGIDVGAKFDIYNLLGELTRQGKALVVVSSDLRELMLICDRIGVLSAGSLIDTFDRD 486

Query: 500 EATQEKVMQLA 510
             TQ++++  A
Sbjct: 487 SWTQDELLAAA 497



 Score = 86.3 bits (212), Expect = 2e-21
 Identities = 60/226 (26%), Positives = 110/226 (48%), Gaps = 5/226 (2%)

Query: 287 VFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFGITPSSSGQITLDGKAVRISDPHMAIE 346
           V   +   L  GE+L + G  G+G++ +++ I G+   ++GQ+   G+  R      A  
Sbjct: 23  VLAGIDLTLMRGEVLALTGENGAGKSTLSKIIGGLVTPTTGQMQYQGQDYRPGSRAQAEA 82

Query: 347 KGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTP 406
            G  ++ ++  L    P LSV EN+ +  LP  +  G+I +K LR    +    + +   
Sbjct: 83  LGIRMVMQELNL---LPTLSVAENLFLDNLP--SKGGWISRKQLRKAAIEAMAHVGLDAI 137

Query: 407 SLEQCIDTLSGGNQQKALLARWLMTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMA 466
             +  +  L  G+QQ   +AR L+ +  +LILDEPT  +       ++  I  L S G++
Sbjct: 138 DPDTLVGELGIGHQQMVEIARNLIGDCHVLILDEPTAMLTAREVEMLFEQITRLQSRGVS 197

Query: 467 VIMISSELPEVLGMSDRVMVMHEGELMGTLDRSEATQEKVMQLASG 512
           +I IS  L E+  ++ R+ V+ +G L+     +    E+++ L  G
Sbjct: 198 IIYISHRLEELARVAQRIAVLRDGNLVCVEPMANYNSEQLVTLMVG 243


Lambda     K      H
   0.320    0.136    0.381 

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: 598
Number of extensions: 29
Number of successful extensions: 7
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: 517
Length of database: 517
Length adjustment: 35
Effective length of query: 482
Effective length of database: 482
Effective search space:   232324
Effective search space used:   232324
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)
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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