GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltJ in Desulfovibrio vulgaris Hildenborough

Align Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized)
to candidate 206177 DVU0751 amino acid ABC transporter, permease protein, His/Glu/Gln/Arg/opine family

Query= TCDB::Q9I403
         (248 letters)



>MicrobesOnline__882:206177
          Length = 596

 Score =  160 bits (406), Expect = 4e-44
 Identities = 94/239 (39%), Positives = 142/239 (59%), Gaps = 12/239 (5%)

Query: 3   YNWDWGVFF-KSTGIGSETYLDWYIAGLGWTIAIALVGWIIALALGSLLGVMRT---VPN 58
           Y + W + F ++T  G+   L+  + GLG T+ I+L+   +AL LG++LG+ R     P 
Sbjct: 35  YQFQWDILFTRNTTYGTHLGLE-ILKGLGVTVRISLISSALALGLGTVLGIARLSLFAPL 93

Query: 59  RLVSGIATAYVEIFRNVPLLVQLFIWYFLVPDLLPEGLQTWFKQDLNPTTSAYLSVVVCL 118
           RL    ATA VE FRN PLLVQLF WYF  P +LPE +    ++ L      +    + L
Sbjct: 94  RLT---ATAVVEFFRNTPLLVQLFFWYFAFPAILPENI----RELLFTGNFEFWCATIGL 146

Query: 119 GLFTAARVCEQVRTGIQALPYGQTSAARAMGFRLPQIYRHVLLPQAFRIIIPPLTSEFLN 178
            ++T+A + E +R G+Q++P G   AA + G    Q+ R ++LP AFR IIPPL SEFLN
Sbjct: 147 SVYTSAFMAEVIRAGLQSIPKGLLEAAYSSGLNYVQVLRTIILPMAFRAIIPPLGSEFLN 206

Query: 179 IFKNSSVASLIGLMELLAQTKQTAEFSANLFEAFTLATLIYFTLNMSLMLIMRLVERKV 237
             KNSS+A ++G+ EL  Q++Q    +   FEA + AT++Y +L++ +  I+  V  K+
Sbjct: 207 NMKNSSLAMVVGVAELTWQSQQVESLTFKGFEATSAATVLYLSLSLLISFILNGVNGKM 265



 Score =  110 bits (276), Expect = 5e-29
 Identities = 69/249 (27%), Positives = 122/249 (48%), Gaps = 29/249 (11%)

Query: 3   YNWDWGVFFKSTGIGSETYLDWY------------IAGLGWTIAIALVGWIIALALGSLL 50
           YN++WGV   +      T L W+            + GL +++ +A++   ++  +G ++
Sbjct: 356 YNFNWGVIADNL----RTLLIWHFPNGQSDELFMGLGGLAYSLLMAVIAISVSFFIGLVV 411

Query: 51  GVMRTVPNRLVSGIATAYVEIFRNVPLLVQLFIWYFLVPDLLPEGLQTWFKQDLNPTTSA 110
           G+ RT  NR+       Y+E+ R  PL++ +F  YF +P L             N   + 
Sbjct: 412 GIGRTSDNRICRIPCLLYIELIRGNPLIIVIFWIYFFIPVLF------------NTFFNV 459

Query: 111 YLSVVVCLGLFTAARVCEQVRTGIQALPYGQTSAARAMGFRLPQIYRHVLLPQAFRIIIP 170
           + S  + L LFT A + E VR GIQ +P GQ  AA + G    Q  R ++LPQA + +IP
Sbjct: 460 FWSATIALTLFTGAYLAEIVRAGIQNIPAGQVEAAYSTGLTFVQTMRRIILPQALKQMIP 519

Query: 171 PLTSEFLNIFKNSSVASLIGLMELLAQTKQ-TAEFSANLFEAFTLATLIYFTLNMSLMLI 229
            +  +F+ IFK++S+A ++G++EL    +           E +     +YF    S+ + 
Sbjct: 520 AIVGQFIAIFKDTSLAFVLGVLELTFVAQGINNRLMVYPMEIYGTVAFLYFICCWSMSVY 579

Query: 230 MRLVERKVA 238
              +ER+++
Sbjct: 580 AARLERRLS 588


Lambda     K      H
   0.327    0.141    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: 420
Number of extensions: 29
Number of successful extensions: 5
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 (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