GapMind for catabolism of small carbon sources

 

Alignments for a candidate for TRET1 in Sphingomonas koreensis DSMZ 15582

Align Facilitated trehalose transporter Tret1; PvTret1 (characterized)
to candidate Ga0059261_1777 Ga0059261_1777 MFS transporter, sugar porter (SP) family

Query= SwissProt::A5LGM7
         (504 letters)



>FitnessBrowser__Korea:Ga0059261_1777
          Length = 458

 Score =  186 bits (471), Expect = 2e-51
 Identities = 131/446 (29%), Positives = 215/446 (48%), Gaps = 26/446 (5%)

Query: 44  ILAAIAVSMGSMVVGFASAYTSPALVSMQNTTITSFKVTEQEASWVGGIMPLAGLAGGIA 103
           IL+A   ++G ++ GF +A  S A  ++Q      F +T+    +      +  + G + 
Sbjct: 23  ILSAAGAALGGLLFGFDTAVISGATQALQ----LQFGLTDAMLGFTVASALIGTVLGSLI 78

Query: 104 GGPFIEYLGRKNTILATAVPFIVAWLLIAFANSIWMVLAGRALSGFCVGIASLSLPVYLG 163
            G   +  GRK  +L  A+ ++V+ L    A  +   L  R + G  +G AS+  P+Y+ 
Sbjct: 79  AGAPADRFGRKGVMLTVAIAYVVSSLGTGLAPDLNAFLVFRFMGGLAIGAASVVTPIYIA 138

Query: 164 ETVQPEVRGTLGLLPTAFGNIGILICFVAGKY--------VNWSGLAFIGSILPIPFMVL 215
           E      RG L  +      +GILI F++           V W  +  I ++    F+++
Sbjct: 139 EVSPARFRGRLVAMNQLNIVLGILIAFLSNYIIAGLVQYDVAWRWMFGIVAVPSTIFLLV 198

Query: 216 TLLIPETPRWFVTRGREERARKALQWLRGKKADVEPELKGIVKSHCEAERHASQNAIFDL 275
           TLL+PE+PRW    G+ +RAR  +Q L    AD   EL  I  +    E          L
Sbjct: 199 TLLLPESPRWLAIHGQADRARDVMQRLGF--ADPRAELARIELAEAREEAAGKPR----L 252

Query: 276 MKRSNLKPLLIALGLMFFQQLSGINAVIFYTVSIFKDAGSTIDENLC-TIIVGVVNFGAT 334
            +RS+  P+  A+ +  F QLSGINA+++Y   IF+ AG+  D  L  +I VG  N   T
Sbjct: 253 FQRSHFTPVACAIAIAMFNQLSGINALLYYAPRIFELAGAGADSALLQSIAVGGTNLVFT 312

Query: 335 FFATVLIDRLGRKILLYISEVAMVITLLTLGTFFYYKNSGNDVSNIGWLPLASFVIYVIG 394
             A  LIDR GR+ LL++  V    TLL +G  +  +++  D    G L L   + ++  
Sbjct: 313 VAALFLIDRFGRRPLLFVGSVICAATLLLVG--WQLESAKPD----GTLILFGLLGFIAA 366

Query: 395 FSSGVGPIPWLMLGEILPGKIRGSAASVATGFNWTCTFIVTKTFADIVAAIGNHGAFWFF 454
           F+   G + W+ + E+ P  +RG   ++ +  +W     +T  F    A++G    F FF
Sbjct: 367 FAMSQGAVIWVFISEVFPSAVRGKGQALGSTTHWVMAAAITWAFPVFAASVGG-WVFAFF 425

Query: 455 GVICLIGLFFVIFFVPETQGKSLEEI 480
           G + L+ L +   F+PET G +LE++
Sbjct: 426 GAMMLLQLLWTWKFMPETNGIALEDM 451


Lambda     K      H
   0.326    0.141    0.428 

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: 570
Number of extensions: 32
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: 504
Length of database: 458
Length adjustment: 34
Effective length of query: 470
Effective length of database: 424
Effective search space:   199280
Effective search space used:   199280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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