GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate 8500595 DvMF_1343 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= reanno::Smeli:SMc02119
         (397 letters)



>FitnessBrowser__Miya:8500595
          Length = 337

 Score = 92.8 bits (229), Expect = 1e-23
 Identities = 48/121 (39%), Positives = 75/121 (61%)

Query: 271 LALSFYTAAFIAEIVRAGIRGVSKGQTEAAHALGIRPALTTRLVVVPQAMRIIIPPLTSQ 330
           +AL+ +T A++AEIVRAGI+ V +GQ EAA +LG+  A   R V++PQA R I+PPL  Q
Sbjct: 214 MALALFTGAYVAEIVRAGIQSVHRGQMEAARSLGMNYAQAMRKVILPQAFRRIMPPLAGQ 273

Query: 331 YLNLTKNSSLAVAIGYADLVAVGGTILNQTGQSIEIVSIWLIVYLSLSLATSLFMNWYNA 390
           +++L K+SSL   I   +L      ++  + Q  E+  +  ++YL L+   SLF+ +   
Sbjct: 274 FISLIKDSSLLGVIAIRELTKATREVVTTSLQPFELWIVCAVLYLVLTFTLSLFVQYLER 333

Query: 391 R 391
           R
Sbjct: 334 R 334



 Score = 48.9 bits (115), Expect = 2e-10
 Identities = 48/181 (26%), Positives = 82/181 (45%), Gaps = 50/181 (27%)

Query: 19  INDPQVRG--IFYQAITIIILAALI--YWIVDNTVDNLRRANIASGYDFV------RSRA 68
           ++ P+ RG  +F++A+ +  + AL+  +W+  ++V+ + R N    Y +V      R+ A
Sbjct: 7   LDKPKGRGFFLFWKAMFVAAMLALVAFFWVASSSVEYIWRWNRVPQYFWVNEAADVRAEA 66

Query: 69  GFDV---------------------------GQSLISFTS-DSTY-----GR-------A 88
             DV                           G+S +  +S D TY     GR        
Sbjct: 67  EGDVTIIDRQGNEQRVVVRDASGEEHTHLLPGESKVLVSSGDFTYRGDVLGRYQLNRPGI 126

Query: 89  LLVGFINTLLVAITGIITATIIGFIVGIGRLSHNWIIAKLSLAYVEVFRNIPPLLVIFFW 148
           LL G   TL V++  II   +IG + G+ R+S N ++   ++ Y+E+ R  P L+ IF W
Sbjct: 127 LLEGLWITLEVSVLAIIGGIVIGVVTGLCRISINPMLRWGAITYIEIIRGSPLLVQIFLW 186

Query: 149 Y 149
           Y
Sbjct: 187 Y 187


Lambda     K      H
   0.327    0.141    0.412 

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: 324
Number of extensions: 18
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 397
Length of database: 337
Length adjustment: 30
Effective length of query: 367
Effective length of database: 307
Effective search space:   112669
Effective search space used:   112669
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 (21.7 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