Alignments for a candidate for gltJ in Desulfovibrio vulgaris Hildenborough

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 paper from 2022 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

GapMind for catabolism of small carbon sources