GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PS417_04205 in Escherichia coli BW25113

Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate 17750 b3691 D-galactonate transport (VIMSS)

Query= reanno::WCS417:GFF828
         (454 letters)



>FitnessBrowser__Keio:17750
          Length = 430

 Score =  383 bits (984), Expect = e-111
 Identities = 193/434 (44%), Positives = 276/434 (63%), Gaps = 9/434 (2%)

Query: 1   MQATKPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAY 60
           + A KP   RYL L+M+F+   I Y DRA +A+A + +Q++ GI    +GY+FSAF W Y
Sbjct: 5   VNAAKPGRRRYLTLVMIFITVVICYVDRANLAVASAHIQEEFGITKAEMGYVFSAFAWLY 64

Query: 61  VAGQIPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAE 120
              QIPGGW LDR GS+  Y ++IF WS+ T+ QG+      +T +++L  LR + G+ E
Sbjct: 65  TLCQIPGGWFLDRVGSRVTYFIAIFGWSVATLFQGF------ATGLMSLIGLRAITGIFE 118

Query: 121 APSFPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGV 180
           AP+FP N R+V +WFP  ER +A   + S Q+       PL+ WI     W  VFIV G 
Sbjct: 119 APAFPTNNRMVTSWFPEHERASAVGFYTSGQFVGLAFLTPLLIWIQEMLSWHWVFIVTGG 178

Query: 181 IGIIFSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQL 240
           IGII+SLIW KV   PR    I++AE ++I   G +VD D    K  +      D+  +L
Sbjct: 179 IGIIWSLIWFKVYQPPRLTKGISKAELDYIRDGGGLVDGDAPVKKEARQPLTAKDW--KL 236

Query: 241 LTNRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLG 300
           + +R ++GVYLGQ+ +    +FFLTWFP YL Q++G+T LKAGF+ ++P +  F+G +L 
Sbjct: 237 VFHRKLIGVYLGQFAVASTLWFFLTWFPNYLTQEKGITALKAGFMTTVPFLAAFVGVLLS 296

Query: 301 GVISDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGAL 360
           G ++D L+RKG SL FARK PII GLLIS+ I+  NY +   M++  MALAFFG G  ++
Sbjct: 297 GWVADLLVRKGFSLGFARKTPIICGLLISTCIMGANYTNDPMMIMCLMALAFFGNGFASI 356

Query: 361 GWAVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVA 420
            W++VS  +P ++ GL+GG+FN  G L  IT P+V+GY+    G F  ALV++ A AL+ 
Sbjct: 357 TWSLVSSLAPMRLIGLTGGVFNFAGGLGGITVPLVVGYLAQGYG-FAPALVYISAVALIG 415

Query: 421 VFSYLVIVGPIKRV 434
             SY+++VG +KRV
Sbjct: 416 ALSYILLVGDVKRV 429


Lambda     K      H
   0.327    0.142    0.444 

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: 683
Number of extensions: 41
Number of successful extensions: 5
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: 454
Length of database: 430
Length adjustment: 32
Effective length of query: 422
Effective length of database: 398
Effective search space:   167956
Effective search space used:   167956
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: 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