GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdX in Paraburkholderia bryophila 376MFSha3.1

Align D-serine transporter DsdX; D-serine-specific permease (characterized)
to candidate H281DRAFT_04276 H281DRAFT_04276 gluconate permease GntT

Query= SwissProt::A0A0H2VAP9
         (445 letters)



>FitnessBrowser__Burk376:H281DRAFT_04276
          Length = 461

 Score =  311 bits (797), Expect = 3e-89
 Identities = 178/457 (38%), Positives = 261/457 (57%), Gaps = 22/457 (4%)

Query: 9   STLL----ISIVLIVLTIVKFKFHPFLALLLASFFVGTMMGMGPLDMVNAIESGIGGTLG 64
           STLL    I+I L++L I ++K +PFL L++ S  +G   GM    +V + E+G G TLG
Sbjct: 7   STLLVFGVIAIALLILLITRYKVYPFLVLIIVSLLLGLASGMPMATIVKSFETGNGNTLG 66

Query: 65  FLAAVIGLGTILGKMMEVSGAAERIGLTLQRCRWLSADVI---MVLVGLICGITLFVEVG 121
            +A V+GLGT+LGKMM  SG AERI  TL    W     I   M++V +I G+ +F EVG
Sbjct: 67  HIAVVVGLGTMLGKMMAESGGAERIATTL--INWFGEKNIHWAMMVVAIIVGLPVFFEVG 124

Query: 122 VVLLIPLAFSIAKKTNTSLLKLAIPLCTALMAVHCVVPPHPAALYVANKLGADIGSVIVY 181
            VLLIP+AF++AK+TN SLL + +P+   L  VH ++PPHPAA+    +  ADIG  I Y
Sbjct: 125 FVLLIPIAFNVAKRTNKSLLLVGLPMVAGLSVVHGLIPPHPAAMLAVQQYHADIGKTIAY 184

Query: 182 GLLVGLMASLIGGPLFLKFLGQRLPFKPVPTEFADLKVRDE------------KTLPSLG 229
           GL++G+  +++ GPLF   + + +         A     D+            + LPS G
Sbjct: 185 GLIIGVPTAIVAGPLFALLISRYVKLPQENALAAQFLGHDDAAKNGATNTAPKRELPSFG 244

Query: 230 ATLFTVLLPIALMLVKTIAELNMARESGLYTLLEFIGNPITATFIAVFVAYYVLGIRQHM 289
            TLFTVLLP+ LMLV + A+L    ++    LL F+GN   A  IAV V+++  G  +  
Sbjct: 245 ITLFTVLLPVILMLVGSWADLVFTPKTLPNDLLHFVGNSDVALLIAVLVSFWTFGASRGF 304

Query: 290 SMGTMLTHTENGFGSIANILLIIGAGGAFNAILKSSSLADTLAVILSNMHMHPILLAWLV 349
           +   +          IA I LI+GAGG F  +L  S ++  +    +  H+ P+L  WLV
Sbjct: 305 NRDQIQKFCGECLAPIAGITLIVGAGGGFGRVLMDSGISKEIVAAATAAHLSPLLFGWLV 364

Query: 350 ALILHAAVGSATVAMMGATAIVAPMLPLY-PDISPEIIAIAIGSGAIGCTIVTDSLFWLV 408
           A ++  A GSATVAM  A  IVAP+       + PE++ +A GSG++  + V D  FWL+
Sbjct: 365 AALIRLATGSATVAMTTACGIVAPIAAASGVQVKPELLVLATGSGSLIFSHVNDGGFWLI 424

Query: 409 KQYCGATLNETFKYYTTATFIASVIALAGTFLLSFII 445
           K+Y G T+ +TFK ++    I S++ L  TF L+ ++
Sbjct: 425 KEYFGMTVGQTFKTWSLLETIISLMGLGLTFALAAVL 461


Lambda     K      H
   0.328    0.142    0.417 

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: 555
Number of extensions: 34
Number of successful extensions: 6
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 445
Length of database: 461
Length adjustment: 33
Effective length of query: 412
Effective length of database: 428
Effective search space:   176336
Effective search space used:   176336
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 (21.8 bits)
S2: 51 (24.3 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