GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_11895 in Acidovorax sp. GW101-3H11

Align Inositol transport system permease protein (characterized)
to candidate Ac3H11_1841 Ribose ABC transport system, ATP-binding protein RbsA (TC 3.A.1.2.1)

Query= reanno::WCS417:GFF2333
         (340 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1841
          Length = 892

 Score =  171 bits (434), Expect = 5e-47
 Identities = 115/346 (33%), Positives = 180/346 (52%), Gaps = 29/346 (8%)

Query: 1   MNAIT-DNKPATVPTKS---RRRLPTELSIFLVLIGIGLVFELFGWIVRDQSFLMNSQRL 56
           MNA T    PA  P+ +   R +L T L +  VL G+  +F           +  +++  
Sbjct: 563 MNAPTAPAAPAATPSSASVWRSQLGTYLGLLAVLAGMVALFSSLS------EYFWSAETF 616

Query: 57  VLMILQVSIIGLLAIGVTQVIITTGIDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTD 116
           + +  ++  + ++A+G+T V+I  GIDLS GSV+AL+A  +A+         A+      
Sbjct: 617 ITIANEIPALAVMAVGMTFVLIIAGIDLSVGSVMALAAATSAA---------AILQWGWT 667

Query: 117 LPVWIPVAMGLGVGLLAGAINGSIIAVTGIPPFIATLGMMVSARGLARYYTE------GQ 170
           +P     A+ L  GL+ G I G+I     +P FI +LGM+ + RG A   T+      G 
Sbjct: 668 VPA--AAALALATGLVCGTITGAISVAWRLPSFIVSLGMLEAVRGSAYVVTDSRTQYVGD 725

Query: 171 PVSMLSDSYTAIGHGAMPVIIFLVVAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVK 230
            +S LS  +   G  +   ++ +V+ V+  + L  T +G+    IG N +A R +G++ +
Sbjct: 726 AISWLSAPF--FGGISFAFLLAVVLVVVAQLVLSRTVFGRCVVGIGTNEEAMRLAGVDPR 783

Query: 231 RHLIIVYSIAGLLAGLAGVVASARAATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITG 290
              +IV+++ GLLAGLAG++ SAR        G   EL  IAA VIGGTSL GG G +  
Sbjct: 784 PIRVIVFAMTGLLAGLAGLMQSARLEAADPNAGTGMELQVIAAVVIGGTSLMGGRGSVVN 843

Query: 291 TVIGALILGVMASGFTFVGVDAYIQDIIKGLIIVVAVVIDQYRNKR 336
           T  G LI+ V+ +G   VG     + II G +IV AV++D  R +R
Sbjct: 844 TAFGVLIIAVLEAGLAQVGASEPSKRIITGFVIVAAVIVDTLRQRR 889


Lambda     K      H
   0.325    0.140    0.394 

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: 544
Number of extensions: 20
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 340
Length of database: 892
Length adjustment: 36
Effective length of query: 304
Effective length of database: 856
Effective search space:   260224
Effective search space used:   260224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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