Alignments for a candidate for PS417_11890 in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for PS417_11890 in Pseudomonas simiae WCS417

Align Inositol transport system ATP-binding protein (characterized)
to candidate GFF4164 PS417_21330 L-arabinose transporter ATP-binding protein

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



>FitnessBrowser__WCS417:GFF4164
          Length = 499

 Score =  394 bits (1012), Expect = e-114
 Identities = 207/491 (42%), Positives = 322/491 (65%), Gaps = 7/491 (1%)

Query: 24  LEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLR 83
           L    I K FPGV AL+ +    RP  V ALMGENGAGKSTL+KI+ G Y P +G +++ 
Sbjct: 6   LRFNGIGKEFPGVKALSQISFEARPREVHALMGENGAGKSTLLKILGGAYLPSSGTLQIG 65

Query: 84  GKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRCTAE 143
            + + F++   +   G+A+IHQEL+L+P M++AEN+++G        +VN  ++ +    
Sbjct: 66  EQTMDFKSAADSIACGVAVIHQELHLVPEMTVAENLFLGHLPTR-FGVVNRSQLRKQALA 124

Query: 144 LLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSII 203
            L  L   +DP+E++G LS+ +RQ+VEIAKA+S  + ++  DEPTS+++ +E+  L +II
Sbjct: 125 CLKGLADEIDPDEKLGRLSLGQRQLVEIAKALSRGAHVIAFDEPTSSLSAREIDRLMAII 184

Query: 204 ADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNS---DSLISMMVGRE 260
             L+ +GK ++Y++H+M EVF I + V VF+DG Y+  +  D MN+   D L++ MVGR+
Sbjct: 185 TRLRDEGKVVLYVSHRMEEVFRICNAVTVFKDGRYV--RTFDDMNALSHDQLVTCMVGRD 242

Query: 261 LSQLFPLRETPIGDLLLTVRDLTLDGVFKDVSFDLHAGEILGIAGLMGSGRTNVAETIFG 320
           +  ++  R+   G++ L V  L   G+ + VS ++H GEILG+ GL+G+GRT +   + G
Sbjct: 243 IQDIYDYRQREQGEVALKVEGLLGPGLREPVSLNVHKGEILGLFGLVGAGRTELFRLLSG 302

Query: 321 ITPSSSGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLENMEMAVLPHYT 380
           +T S++G + L G+ +++  P  AI  G  L  EDRK  G+ P  SV EN+ ++    ++
Sbjct: 303 LTRSTAGSLALCGQTLQLRSPRDAIAAGVLLCPEDRKKEGIIPLSSVAENINISARGAHS 362

Query: 381 GNGFIQQKALRALCED-MCKKLRVKTPSLEQCIDTLSGGNQQKALLARWLMTNPRLLILD 439
             G++ +        D   K ++VKTP+ EQ I  LSGGNQQKA+L RWL    ++L+LD
Sbjct: 363 TFGWLLRDGWETTNADRQIKAMKVKTPNAEQKIMYLSGGNQQKAILGRWLSMPMKVLLLD 422

Query: 440 EPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHEGELMGTLDRS 499
           EPTRGID+GAK+EIY++I  LA+ G+AVI++SS+L EV+G+SDR++VM EG L G L R 
Sbjct: 423 EPTRGIDIGAKSEIYQIIHNLAASGIAVIVVSSDLMEVMGISDRILVMSEGALTGELTRD 482

Query: 500 EATQEKVMQLA 510
           +A + +++QLA
Sbjct: 483 QADEARLLQLA 493



 Score = 81.3 bits (199), Expect = 8e-20
 Identities = 55/224 (24%), Positives = 108/224 (48%), Gaps = 6/224 (2%)

Query: 42  VQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDAGEIRLRGKPIVFETPLAAQKAGIA 101
           V L V  G +L L G  GAG++ L ++++G+ +  AG + L G+ +   +P  A  AG+ 
Sbjct: 273 VSLNVHKGEILGLFGLVGAGRTELFRLLSGLTRSTAGSLALCGQTLQLRSPRDAIAAGVL 332

Query: 102 MIHQELN---LMPHMSIAENIWIGREQLNSLH---MVNHREMHRCTAELLARLRINLDPE 155
           +  ++     ++P  S+AENI I     +S     + +  E      ++ A      + E
Sbjct: 333 LCPEDRKKEGIIPLSSVAENINISARGAHSTFGWLLRDGWETTNADRQIKAMKVKTPNAE 392

Query: 156 EQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLFSIIADLKSQGKGIVY 215
           +++  LS   +Q   + + +S    +L++DEPT  I     + ++ II +L + G  ++ 
Sbjct: 393 QKIMYLSGGNQQKAILGRWLSMPMKVLLLDEPTRGIDIGAKSEIYQIIHNLAASGIAVIV 452

Query: 216 ITHKMNEVFAIADEVAVFRDGHYIGLQRADSMNSDSLISMMVGR 259
           ++  + EV  I+D + V  +G   G    D  +   L+ + + R
Sbjct: 453 VSSDLMEVMGISDRILVMSEGALTGELTRDQADEARLLQLALPR 496


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: 606
Number of extensions: 29
Number of successful extensions: 9
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 3
Number of HSP's successfully gapped: 2
Length of query: 517
Length of database: 499
Length adjustment: 34
Effective length of query: 483
Effective length of database: 465
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 Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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 2024 update 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