GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Ac3H11_2555 in Pseudomonas fluorescens GW456-L13

Align ABC transporter for L-Histidine, periplasmic substrate-binding component 1 (characterized)
to candidate PfGW456L13_1692 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1692
          Length = 258

 Score =  117 bits (294), Expect = 2e-31
 Identities = 81/250 (32%), Positives = 124/250 (49%), Gaps = 14/250 (5%)

Query: 8   LLASLAAAAFCTTGAQAQDNVLRVGTDATFPPMEF-VENGKRTGFDIELVEAIAKTMGKQ 66
           L+  LA +    +   A +  LR+G +A +PP     + G+  GFD ++  A+   M  +
Sbjct: 6   LITGLALSLLACSSVFAAEKTLRIGIEAAYPPFASKTDKGEIVGFDYDIGNALCAQMKAK 65

Query: 67  VEWVDIDFKGLIPGLISKRFDMAVSAIYITDERKKVVDFTDSYYAGGLVVMVKADNKAIN 126
             WV+ +F GLIP L  K+ DMA+S++ I ++RKK VDFT  YY     +++K      +
Sbjct: 66  CVWVEGEFDGLIPSLKVKKIDMALSSMTINEDRKKSVDFTHKYYFTSSRLVMKDGAVVDD 125

Query: 127 KLADLDGKKVSVQVGTKSVSYLTEKF-PKVQRVE-VEKNQEMFNLVDIGRADAAVT---- 180
           + A L GK V VQ  T +  Y +E F PK   V+    N+E++  +  GR DA       
Sbjct: 126 QYASLKGKTVGVQRATTTDRYASEVFEPKGINVKRYSNNEEIYMDLAAGRLDAIFADTIP 185

Query: 181 -----GKPAAFQYVRTRPGLRVLDEQLTTEEYGMALRKDTPELTKAVNGAITKLKADGTY 235
                  P    Y    P L+  D +   E  G+A+RK   EL   +N AI  ++A G Y
Sbjct: 186 LNDFLSMPRGKGYAFVGPELK--DPKYVGEGAGIAVRKGNTELVSELNTAIDGIRASGEY 243

Query: 236 AAIVKKWFSN 245
             I +K+F +
Sbjct: 244 QKISEKYFKS 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: 140
Number of extensions: 9
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: 258
Length adjustment: 24
Effective length of query: 225
Effective length of database: 234
Effective search space:    52650
Effective search space used:    52650
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