GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatQ 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)



>FitnessBrowser__Miya:8502073
          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.

Links

Downloads

Related tools

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