GapMind for catabolism of small carbon sources

 

Alignments for a candidate for AZOBR_RS08235 in Phaeobacter inhibens BS107

Align L-proline and D-alanine ABC transporter, permease component 1 (characterized)
to candidate GFF1633 PGA1_c16550 putative branched-chain amino acid transport system, permease component

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



>FitnessBrowser__Phaeo:GFF1633
          Length = 306

 Score =  144 bits (364), Expect = 2e-39
 Identities = 95/309 (30%), Positives = 157/309 (50%), Gaps = 31/309 (10%)

Query: 5   LQQLINGLSLGAIYGLIAIGYTMVYGIIGMINFAHGEIYMIGAFVALITFLAIGSLGITW 64
           L+Q++NGL  G +  L+A G T+V+G++G+IN AHG +YM+GAF A +     GS     
Sbjct: 7   LEQILNGLQFGVMLFLMAAGLTLVFGVMGLINLAHGALYMVGAFAAAVVAAWTGS----- 61

Query: 65  VPLALLVMLVASMLFTAVYGWTVERIAYRPLRSSPRLAPLISAIGMSIFLQNYVQILQGA 124
                ++ L+AS+   A  G  VE +  R L     L  +++   + +      + + G 
Sbjct: 62  ----FVLALMASLAAAAAAGALVEFLVIRKLYDRDHLDQVLATFALILIFSEGTRWVFG- 116

Query: 125 RSKPLQPILPGNLT---LMDGAVSVSYVRLATIVITIALMYGFTQLITRTSLGRAQRACE 181
            S PL   +P  L+    + G +     RL  I I + +  G   LI RT +G   RA E
Sbjct: 117 -SFPLFLDVPSYLSGPISLPGGIEYPLYRLTIIAIGLVVAAGLFWLIARTRIGIQIRAGE 175

Query: 182 QDKKMAGLLGVNVDRVISLTFVMGAALAAVAGMMVLLIYGVIDFYIGFLAGVKAFTAAVL 241
            D++M   LGV++ ++ +L F +GAALA +AG +V  I  V    +G    + AF   V+
Sbjct: 176 SDREMIAALGVDISKLYTLVFALGAALAGLAGALVGAIQSV-QVGMGEPVLILAFVVIVI 234

Query: 242 GGIGSLPGAMLGGVVIGLIEAFWSGYM----------------GSEWKDVATFTILVLVL 285
           GGIGS+ GAM+G +++GL +     ++                G+    +  + ++ ++L
Sbjct: 235 GGIGSIKGAMVGALLVGLTDTLGGVFLPQMFALFMEPASATSVGASLASMLIYILMAVIL 294

Query: 286 IFRPTGLLG 294
           + RP+GL G
Sbjct: 295 LVRPSGLYG 303


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: 295
Number of extensions: 22
Number of successful extensions: 5
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: 306
Length adjustment: 27
Effective length of query: 274
Effective length of database: 279
Effective search space:    76446
Effective search space used:    76446
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