GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_17590 in Pseudomonas fluorescens GW456-L13

Align ABC transporter substrate-binding protein; SubName: Full=Histidine transport system substrate-binding protein (characterized, see rationale)
to candidate PfGW456L13_4635 Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)

Query= uniprot:A0A1N7UK26
         (258 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4635
          Length = 260

 Score =  275 bits (702), Expect = 9e-79
 Identities = 136/253 (53%), Positives = 180/253 (71%)

Query: 4   LRSLFAALLLPLCATAHAQEWKEIRFGVFPEYPPFESVAADGSLQGFDIELGNAICAKLE 63
           L +L A  L     +A A+E+KE+RFGV P Y PFES AADGSL GFDI+LGNAICA+L+
Sbjct: 5   LLTLSALALCMAAGSAMAKEYKELRFGVDPSYAPFESKAADGSLVGFDIDLGNAICAELK 64

Query: 64  VKCTWVHNEFDGMIPALRARKFDAIMSSMAVTPAREKIIDFSDRLFLSPTSVITRKSADF 123
           VKC WV ++FDGMIP L+A KFD ++SSM VTPAREK+IDFS  LF  PT+ + +K +  
Sbjct: 65  VKCKWVESDFDGMIPGLKANKFDGVISSMTVTPAREKVIDFSSELFSGPTAYVFKKGSGL 124

Query: 124 GDTPESLMGKQVGVLQGSLQEAYARAHLAKLGAQIKAYQSQDQNYADLQNGRLDATLTDK 183
            +   SL GK VG  QG++QEAYA+A L K G + +AYQ+QDQ Y+DL +GRLDA + D 
Sbjct: 125 TEDVASLKGKTVGYEQGTIQEAYAKAVLDKAGVKTQAYQNQDQVYSDLTSGRLDAAIQDM 184

Query: 184 LEAQLNFLSKPEGSDFKTGPAFKDPTLPLDIAMGLRKNDQALRALINKGIAAVQADGTYA 243
           L+A+L FL  P+G  ++         LP   A+G++K +  L+AL++KGI A+  DGTYA
Sbjct: 185 LQAELGFLKSPKGEGYEVSKPVDSELLPAKTAVGIKKGNTELKALLDKGIKALHDDGTYA 244

Query: 244 QIQKKYFGDQDIY 256
            IQKK+FGD ++Y
Sbjct: 245 TIQKKHFGDLNLY 257


Lambda     K      H
   0.319    0.135    0.393 

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: 204
Number of extensions: 6
Number of successful extensions: 1
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: 258
Length of database: 260
Length adjustment: 24
Effective length of query: 234
Effective length of database: 236
Effective search space:    55224
Effective search space used:    55224
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: 47 (22.7 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