GapMind for catabolism of small carbon sources

 

Alignments for a candidate for SSS-glucose in Dinoroseobacter shibae DFL-12

Align Sodium/glucose cotransporter 5; Na(+)/glucose cotransporter 5; Solute carrier family 5 member 10 (characterized)
to candidate 3610523 Dshi_3904 SSS sodium solute transporter superfamily (RefSeq)

Query= SwissProt::Q6R4Q5
         (597 letters)



>FitnessBrowser__Dino:3610523
          Length = 526

 Score =  281 bits (720), Expect = 4e-80
 Identities = 173/528 (32%), Positives = 275/528 (52%), Gaps = 61/528 (11%)

Query: 17  LTVVDIAIIAVYFALNVAVGIWSSCRASRNTVRGYFLAGRDMTWWPIGASLFASSEGSGL 76
           LT++D  +IAVY A+ +A+G+W + +    T    FLAGR + W  IG SLFAS+  +  
Sbjct: 9   LTMLDYGVIAVYLAIVIAIGVWVARKT--RTGEDLFLAGRSLGWAAIGFSLFASNISTST 66

Query: 77  FIGLAGSGAAGGLAVAGFEWNATYVLLALAWVFVPIYLSSEIVTMPEYMQKRYGGQRIRM 136
            +GL GS   GGL V+ +EW A   LL +A++F P++L S I T PEY++ RY  +R+R+
Sbjct: 67  LVGLTGSAYTGGLTVSSYEWMAGIPLLFMAFIFAPVFLKSRISTTPEYLENRY-SRRVRL 125

Query: 137 YLSVLSLLLSVFTKISIDLYAGALFVHICL-GWNFYLSTVIMLAITALYTIAGGLTAVIY 195
           Y S L+++ +V    +  LYAGA+ + +     + ++S V +     +YT  GGL AV+Y
Sbjct: 126 YFSGLTIVFTVIVDTAGGLYAGAVVLKVFFPDLDIWMSCVAIGLFAGIYTATGGLRAVVY 185

Query: 196 TDALQTLVMVAGAVILTIKAFEQIGGYEQLAEAYAQAVPSRTISNTTCHVPRADAMHMFR 255
           TD LQ +V++ G  +     ++ +   +   E+    VP   +S                
Sbjct: 186 TDILQAVVLICGTGLTAFLMYQSV---DFSWESVRSQVPEGHLS--------------IV 228

Query: 256 DPYTAD-LPWTGMTFGLTIMAAWYWCTDQVIVQRSLSARDLNHAKGGSILASYLKMLPMG 314
            P   D LPW G+  G+ ++  WYW T+Q IVQR L A+DL++A+ G+IL   LK+LP  
Sbjct: 229 QPIDDDTLPWPGLFTGVWLLGFWYWVTNQYIVQRVLGAKDLSNAQWGAILGGILKILPTF 288

Query: 315 LMVMPGMISRVLFPDDVGCVVPAECLRACGAEIGCSNIAYPKLVMELMPTGLRGLMVAVM 374
            +++PG+++ V  PD                 I  S+  +P ++ E++P+GL GL++A +
Sbjct: 289 FIILPGVMALVTLPD-----------------IQNSDQVFPIIITEVLPSGLTGLVMAGL 331

Query: 375 MAALMSSLTSIFNSSSTLFTMDIWRRLRPRAGERELLLVGRLVIVVLVGVSVAWIPVLQG 434
           +AA+MS++ S  NSSSTL   D   R             G +  +  + +++AW P++Q 
Sbjct: 332 IAAIMSTVDSTLNSSSTLLINDFLTRPEKEPDPETAKKWGMMATLGFMVIAIAWAPLIQY 391

Query: 435 SNGGQLFIYMQSVTSSLAPPVTAVFVLGIFWRRANEQGAFWGLMAGLAVGATRLVLEFLH 494
             G  L+ Y+Q   S L PP+   F LG  W R  E  AFW L+ G  +G    +L    
Sbjct: 392 FGG--LWAYIQQAFSVLVPPLVVCFTLGALWSRGTENAAFWTLIIGHTLGLVVFMLN--- 446

Query: 495 PAPPCGHPDTRPPILHGVHYLHFAVALFLL---SGAVVVAGSLLTPHP 539
                           G+  LH+ +++ ++   S A+ VA SL    P
Sbjct: 447 --------------QFGIWPLHYTISVTIMTAVSAAIFVALSLRDDTP 480


Lambda     K      H
   0.327    0.139    0.437 

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: 768
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: 597
Length of database: 526
Length adjustment: 36
Effective length of query: 561
Effective length of database: 490
Effective search space:   274890
Effective search space used:   274890
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: 53 (25.0 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