GapMind for catabolism of small carbon sources

 

Alignments for a candidate for artQ in Dechlorosoma suillum PS

Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate Dsui_0636 Dsui_0636 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= reanno::pseudo1_N1B4:Pf1N1B4_3432
         (229 letters)



>FitnessBrowser__PS:Dsui_0636
          Length = 245

 Score =  109 bits (272), Expect = 5e-29
 Identities = 68/218 (31%), Positives = 117/218 (53%), Gaps = 8/218 (3%)

Query: 9   ILDGVWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIPDLVLILLI 68
           +  G+  T+ L+LS+ V+A+V+G I   LR  P RWL+    +Y    R +P LV +   
Sbjct: 25  LFTGLQWTVALSLSAWVIALVVGSIVGVLRTVPNRWLSGFAAVYVECFRNVPLLVQLFSW 84

Query: 69  FYGGQDLLNRVAPMFGYDDYIDLNPLA----AGIGTLGFIFGAYLSETFRGAFMAIPKGQ 124
           ++   +LL    P  G + Y   +PL     A +  LG    A ++E  R    ++P+GQ
Sbjct: 85  YFVLPELL---PPALG-NAYKQSDPLLQQFLAAMLCLGLFTAARVAEQVRAGIESLPRGQ 140

Query: 125 AEAGMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQA 184
             AG+A G +  QV+  VL+P   R+ +P  T+ +L + K +A+ + +GL ++  +A+Q 
Sbjct: 141 RNAGLAMGFTLAQVYRHVLLPMAFRIIVPPLTSEFLNIFKNSAVATTIGLIELSRQAQQL 200

Query: 185 ADATREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSV 222
            D T +P+  F+AV  +Y+ I    +  +R LE++  V
Sbjct: 201 VDYTAQPYEAFIAVTLLYVCINVTVMFLMRRLEEKVRV 238


Lambda     K      H
   0.329    0.144    0.428 

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: 150
Number of extensions: 6
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: 229
Length of database: 245
Length adjustment: 23
Effective length of query: 206
Effective length of database: 222
Effective search space:    45732
Effective search space used:    45732
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: 46 (22.3 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