GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aapQ in Rhodobacter viridis JA737

Align ABC transporter for L-Glutamine, L-Histidine, and other L-amino acids, permease component 1 (characterized)
to candidate WP_110804905.1 C8J30_RS06530 amino acid ABC transporter permease

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



>NCBI__GCF_003217355.1:WP_110804905.1
          Length = 262

 Score = 90.1 bits (222), Expect = 6e-23
 Identities = 66/211 (31%), Positives = 103/211 (48%), Gaps = 16/211 (7%)

Query: 190 TLLAFVIAVAASVFFARYARKRQLATGERLPVLWTVLG-----LIIGLPLVTFLVTGAPI 244
           TL AF  A+   +  A  +  R L        +W  L      +I G+P++  L+  A  
Sbjct: 51  TLFAFAGALVLGLVLAVASLSRHL--------IWRQLARFYTEVIRGVPIIVMLLYVAFA 102

Query: 245 TFDIPVAG--KFNLTGGSVVG-PEFMSLFLALSFYTAAFIAEIVRAGIRGVSKGQTEAAH 301
                VAG     L   SV   P      LAL    AAF+AE+ RAG+  V +GQ EAA 
Sbjct: 103 LVPAVVAGWNALGLPEASVRDFPLLARAVLALILAYAAFLAEVFRAGLLSVERGQIEAAK 162

Query: 302 ALGIRPALTTRLVVVPQAMRIIIPPLTSQYLNLTKNSSLAVAIGYADLVAVGGTILNQTG 361
           ALG+   L  RL++ PQA R ++PPL + ++ + K+SSL   +G AD+  +G        
Sbjct: 163 ALGLNGWLRFRLIIFPQAFRTVLPPLGNDFVAMVKDSSLVSVLGVADITQLGKVTAAGNF 222

Query: 362 QSIEIVSIWLIVYLSLSLATSLFMNWYNARM 392
           +  E  ++  ++YL++++  SL +    A +
Sbjct: 223 RYFETYNVVALIYLAMTVTLSLALRKLEAHL 253



 Score = 35.8 bits (81), Expect = 1e-06
 Identities = 17/71 (23%), Positives = 37/71 (52%)

Query: 96  TLLVAITGIITATIIGFIVGIGRLSHNWIIAKLSLAYVEVFRNIPPLLVIFFWYSGVLSI 155
           T+ V +     A ++G ++ +  LS + I  +L+  Y EV R +P ++++ +    ++  
Sbjct: 47  TVFVTLFAFAGALVLGLVLAVASLSRHLIWRQLARFYTEVIRGVPIIVMLLYVAFALVPA 106

Query: 156 LPQARDALALP 166
           +    +AL LP
Sbjct: 107 VVAGWNALGLP 117


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: 248
Number of extensions: 10
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: 262
Length adjustment: 28
Effective length of query: 369
Effective length of database: 234
Effective search space:    86346
Effective search space used:    86346
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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