GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltJ in Desulfovibrio vulgaris Miyazaki F

Align ABC transporter for L-asparagine and L-glutamate, permease component 1 (characterized)
to candidate 8502073 DvMF_2786 polar amino acid ABC transporter, inner membrane subunit (RefSeq)

Query= reanno::pseudo1_N1B4:Pf1N1B4_772
         (248 letters)



>lcl|FitnessBrowser__Miya:8502073 DvMF_2786 polar amino acid ABC
           transporter, inner membrane subunit (RefSeq)
          Length = 596

 Score =  149 bits (375), Expect = 2e-40
 Identities = 82/235 (34%), Positives = 131/235 (55%), Gaps = 4/235 (1%)

Query: 3   YNWDWGVFFKSTGVGSEIYFDWYLSGLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVS 62
           Y + W + F        +     L GL  T+ I++ +  +ALLLG++LG+ R    R + 
Sbjct: 35  YEFKWSMLFTRNETYGVVMGAEILKGLANTVRISLISSALALLLGTMLGLARLSLFRPLR 94

Query: 63  GIATCYVELFRNVPLLVQLFIWYFLVPDLLPADIQEWYKQDLNPTTSAFLSVVVCLGLFT 122
             ATC +E FRN PLL+QLF WYF  P +LP + +E     L      F    + L ++T
Sbjct: 95  VTATCVIEFFRNTPLLIQLFFWYFAFPAILPDNARE----ALFSIQFEFWCATIGLSIYT 150

Query: 123 TARVCEQVRTGIQALPRGQEAAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKN 182
            + + E +R G+Q++P+G   AA + G    Q+   ++LP A+R IIPPL SEFLN  KN
Sbjct: 151 ASFMAEVIRAGLQSIPKGLLEAAYSSGLSYFQVLRTIILPLAFRAIIPPLGSEFLNNMKN 210

Query: 183 SSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLLMRSVEKKV 237
           SS+A ++G+ EL    +Q    +   FEA + AT++Y +L++ +  ++  V  ++
Sbjct: 211 SSLAMVVGVAELTWHAQQVESLTFKGFEATSAATVLYLSLSLIISFILNGVNGRM 265



 Score =  101 bits (252), Expect = 3e-26
 Identities = 65/226 (28%), Positives = 113/226 (50%), Gaps = 15/226 (6%)

Query: 14  TGVGSEIYFDWYLSGLGWTIAIAVAAWIIALLLGSILGVMRTVPNRIVSGIATCYVELFR 73
           TG   E++    L GL +++ +AV A  ++  +G  +GV R+  NR+       Y+EL R
Sbjct: 377 TGRPDEMFLG--LGGLAYSLLMAVIAISVSFFIGLAVGVGRSSSNRVFRIPCLLYIELIR 434

Query: 74  NVPLLVQLFIWYFLVPDLLPADIQEWYKQDLNPTTSAFLSVVVCLGLFTTARVCEQVRTG 133
             PL++ +F  YF +P +               T + F S    L  FT A + E VRTG
Sbjct: 435 GNPLIIVIFWVYFFIPVMF------------GTTLNVFWSATWALTAFTGAYIAEIVRTG 482

Query: 134 IQALPRGQEAAARAMGFKLPQIYWNVLLPQAYRIIIPPLTSEFLNVFKNSSVASLIGLME 193
           IQ +P GQ  AA + G    Q    ++LPQA + +IP +  +F+ +FK++S+A ++G++E
Sbjct: 483 IQNIPAGQVEAAYSTGLTYLQAMRRIVLPQALKQMIPAIVGQFIAIFKDTSLAFVLGVLE 542

Query: 194 LLAQTKQ-TAEFSANLFEAFTLATLIYFTLNMSLMLLMRSVEKKVA 238
           L    +        +  E +     +YF    S+ +    +E++++
Sbjct: 543 LTFVAQGINNRLMIHPMEIYGTVAFLYFICCYSMSVFAARLERRLS 588


Lambda     K      H
   0.326    0.140    0.433 

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: 393
Number of extensions: 23
Number of successful extensions: 4
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: 248
Length of database: 596
Length adjustment: 30
Effective length of query: 218
Effective length of database: 566
Effective search space:   123388
Effective search space used:   123388
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: 50 (23.9 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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