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 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 (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:

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. 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:

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:

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