GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Acidovorax sp. GW101-3H11

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate Ac3H11_1939 High-affinity branched-chain amino acid transport system permease protein LivH (TC 3.A.1.4.1)

Query= reanno::azobra:AZOBR_RS08235
         (301 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1939
          Length = 291

 Score =  160 bits (406), Expect = 2e-44
 Identities = 102/300 (34%), Positives = 170/300 (56%), Gaps = 13/300 (4%)

Query: 4   FLQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGIT 63
           F+Q LI+G+S G IYGLIA+G+ ++Y     ++FA GE+ M+GAF  L     +G     
Sbjct: 3   FVQLLISGVSQGCIYGLIALGFVLIYKATETVSFAQGELMMLGAFCGLALMTVLG----- 57

Query: 64  WVPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQ- 122
                  V ++AS++   ++G  VER   RP+   P  + ++  IG+   L+  V ++  
Sbjct: 58  ---FPFWVAVLASVVAMGLFGVLVERAVIRPILGQPAFSIVMLTIGIGYVLRGLVTMIPN 114

Query: 123 -GARSKPLQPILPGNLTLMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACE 181
            G  +  L P+   + +L  G + VS  +L  I  T AL      +   + LG A +A  
Sbjct: 115 IGTDTHTL-PVPYKDQSLRLGELVVSAEQLVVIGATGALCVLLFAMFRYSKLGIAMQAAS 173

Query: 182 QDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVL 241
           Q++  A  +G+ V R+  L + + A +AAVAG+++  I   +   +GF+ G+KAF AAV+
Sbjct: 174 QNQLAAYYMGIPVQRLNGLAWGLAAVVAAVAGLLLAPIT-FVHANMGFI-GLKAFPAAVV 231

Query: 242 GGIGSLPGAMLGGVVIGLIEAFWSGYMGSEWKDVATFTILVLVLIFRPTGLLGRPEIEKV 301
           GG GSLPGA++GG+VIG++E+    Y+   +KD A + +++++L+ +P GL G    +KV
Sbjct: 232 GGFGSLPGAIVGGLVIGIVESLSGFYLPDGFKDTAAYIVVLIMLMVKPNGLFGEKLRKKV 291


Lambda     K      H
   0.329    0.144    0.425 

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: 302
Number of extensions: 23
Number of successful extensions: 4
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: 301
Length of database: 291
Length adjustment: 26
Effective length of query: 275
Effective length of database: 265
Effective search space:    72875
Effective search space used:    72875
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 48 (23.1 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