GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2555 in Pseudomonas fluorescens FW300-N1B4

Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate Pf1N1B4_4791 Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)

Query= reanno::acidovorax_3H11:Ac3H11_2555
         (249 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4791
          Length = 259

 Score =  115 bits (287), Expect = 1e-30
 Identities = 81/249 (32%), Positives = 122/249 (48%), Gaps = 11/249 (4%)

Query: 7   LLLASLAAAAFCTTGAQAQD-NVLRVGTDATFPPMEFVE-NGKRTGFDIELVEAIAKTMG 64
           L L +LA    C+TGA A++   LR G + ++PP E    +G   GF ++L  AI   + 
Sbjct: 6   LTLPALALLC-CSTGASAKEWKELRFGVNPSYPPFESTTADGGVQGFGVDLGNAICAELK 64

Query: 65  KQVEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNKA 124
            +  WV  DF GLIP L + +FD   S++ +TD RKK +DFTD  YAG   ++ + D+  
Sbjct: 65  LKCVWVSNDFDGLIPALKAGKFDAIESSMTVTDARKKQIDFTDRLYAGPTAIVTRKDSGL 124

Query: 125 INKLADLDGKKVSVQVGTKSVSYLTEKF-PKVQRVEVEKNQ-EMFNLVDIGRADAAVTGK 182
           +     L GK +    GT   +Y   K  P   ++   +NQ +++  +  GR DA++  K
Sbjct: 125 LPTAESLRGKTIGYMQGTIQETYAKAKLGPGGVKLRAYQNQDQVYADLVFGRLDASIQDK 184

Query: 183 PAAFQYVRTRP------GLRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTYA 236
             A     T P          + + L   E  + +RKD  EL   +N AI  L   G YA
Sbjct: 185 LQAQMSFLTSPQGADFQNSEGISDPLVPSEIAIGIRKDNEELKGMLNAAIKALHEKGIYA 244

Query: 237 AIVKKWFSN 245
            I +K F +
Sbjct: 245 QIQQKHFGD 253


Lambda     K      H
   0.317    0.133    0.369 

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: 145
Number of extensions: 10
Number of successful extensions: 3
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: 249
Length of database: 259
Length adjustment: 24
Effective length of query: 225
Effective length of database: 235
Effective search space:    52875
Effective search space used:    52875
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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