GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for L-Arginine and L-Citrulline, permease component 2 (characterized)
to candidate Ac3H11_3200 Amino acid ABC transporter permease protein

Query= reanno::pseudo1_N1B4:Pf1N1B4_3433
         (232 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3200
          Length = 604

 Score = 88.2 bits (217), Expect = 3e-22
 Identities = 60/207 (28%), Positives = 100/207 (48%), Gaps = 10/207 (4%)

Query: 16  LGGLVTTLKLLALSLFFGLLAALPLGLMRVSKQPVVNMSAWLFTYVIRGTPMLVQLFLIY 75
           L GL  TL L AL   FG      L L RVS+ P++   +W F ++ R  P++V L +I 
Sbjct: 83  LVGLGRTLLLTALGALFGFTLGTALALARVSRSPLLAGLSWTFIWIFRSIPVIVLLLIIN 142

Query: 76  YGLAQFEAVRESFL---WPWLSSAT-------FCACLAFAINTSAYTAEIIAGSLRATPN 125
                +E V        W + S  T         A +   +N +A+ +EI+ G + +   
Sbjct: 143 NLGYLYETVSVGLPFTDWTFFSYPTTQLISPFVAALIGLTLNQAAFASEIVRGGILSVDQ 202

Query: 126 GEIEAAKAMGMSRIKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAAR 185
           G++EAA A+G+ R +   RI+LP A+R  LP   N++I + + TS   I+ L ++    +
Sbjct: 203 GQLEAAAALGLPRRRQAFRIVLPQAMRSILPAGFNDIIGLAKGTSNVYILALPELFYTIQ 262

Query: 186 TVNAQFYLPFEAYITAGVFYLCLTFIL 212
            +  +        + A V+YL +  +L
Sbjct: 263 IIYRRNLEVIPLLMVATVWYLVILTVL 289


Lambda     K      H
   0.330    0.140    0.427 

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: 223
Number of extensions: 8
Number of successful extensions: 2
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: 232
Length of database: 604
Length adjustment: 30
Effective length of query: 202
Effective length of database: 574
Effective search space:   115948
Effective search space used:   115948
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 (21.9 bits)
S2: 49 (23.5 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