GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cscB in Escherichia coli BW25113

Align Sucrose permease; Sucrose transport protein (characterized)
to candidate 14481 b0343 galactoside permease (NCBI)

Query= SwissProt::P30000
         (415 letters)



>FitnessBrowser__Keio:14481
          Length = 417

 Score =  231 bits (590), Expect = 2e-65
 Identities = 123/397 (30%), Positives = 216/397 (54%), Gaps = 12/397 (3%)

Query: 11  YYRFASSYSFLFFISWSLWWSLYAIWLKGHLGLTGTELGTLYSVNQFTSILFMMFYGIVQ 70
           ++ F   + F FFI  + ++  + IWL     ++ ++ G +++     S+LF   +G++ 
Sbjct: 9   FWMFGLFFFFYFFIMGA-YFPFFPIWLHDINHISKSDTGIIFAAISLFSLLFQPLFGLLS 67

Query: 71  DKLGLKKPLIWCMSFILVLTGPFMIYVYEPLLQSNFSVGLILGALFFGLGYLAGCGLLDS 130
           DKLGL+K L+W ++ +LV+  PF I+++ PLLQ N  VG I+G ++ G  + AG   +++
Sbjct: 68  DKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNAGAPAVEA 127

Query: 131 FTEKMARNFHFEYGTARAWGSFGYAIGAFFAGIFFSISPHINFWLVSLFGAVFMMINMRF 190
           F EK++R  +FE+G AR +G  G+A+ A   GI F+I+    FWL S  G   ++  + F
Sbjct: 128 FIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFTINNQFVFWLGS--GCALILAVLLF 185

Query: 191 ---KDKDHQCIAADAGGVKKEDF-----IAVFKDRNFWVFVIFIVGTWSFYNIFDQQLFP 242
               D       A+A G     F     + +F+    W   ++++G    Y++FDQQ F 
Sbjct: 186 FAKTDAPSSATVANAVGANHSAFSLKLALELFRQPKLWFLSLYVIGVSCTYDVFDQQ-FA 244

Query: 243 VFYAGLFESHDVGTRLYGYLNSFQVVLEALCMAIIPFFVNRVGPKNALLIGVVIMALRIL 302
            F+   F + + GTR++GY+ +   +L A  M   P  +NR+G KNALL+   IM++RI+
Sbjct: 245 NFFTSFFATGEQGTRVFGYVTTMGELLNASIMFFAPLIINRIGGKNALLLAGTIMSVRII 304

Query: 303 SCALFVNPWIISLVKLLHAIEVPLCVISVFKYSVANFDKRLSSTIFLIGFQIASSLGIVL 362
             +   +   + ++K LH  EVP  ++  FKY  + F+ R S+TI+L+ F     L ++ 
Sbjct: 305 GSSFATSALEVVILKTLHMFEVPFLLVGCFKYITSQFEVRFSATIYLVCFCFFKQLAMIF 364

Query: 363 LSTPTGILFDHAGYQTVFFAISGIVCLMLLFGIFFLS 399
           +S   G +++  G+Q  +  +  +     L  +F LS
Sbjct: 365 MSVLAGNMYESIGFQGAYLVLGLVALGFTLISVFTLS 401



 Score = 27.3 bits (59), Expect = 9e-04
 Identities = 41/191 (21%), Positives = 79/191 (41%), Gaps = 12/191 (6%)

Query: 215 KDRNFWVFVIFIVGTWSFYNIFDQQLFPVFYAGLFESHDVGTRLYGYLNSFQVVLEALCM 274
           K+ NFW+F +F    + FY       FP F   L + + +     G + +   +   L  
Sbjct: 5   KNTNFWMFGLF----FFFYFFIMGAYFPFFPIWLHDINHISKSDTGIIFAAISLFSLLFQ 60

Query: 275 AIIPFFVNRVGPKNALLIGVVIMALRILSCALFV-NPWI---ISLVKLLHAIEVPLCVIS 330
            +     +++G +  LL  +  M +      +F+  P +   I +  ++  I +  C  +
Sbjct: 61  PLFGLLSDKLGLRKYLLWIITGMLVMFAPFFIFIFGPLLQYNILVGSIVGGIYLGFCFNA 120

Query: 331 VFKYSVANFDKRLSSTIFLIG-FQIASSLGIVLLSTPTGILFDHAGYQTVFFAISGIVCL 389
                 A  +K    + F  G  ++   +G  L ++  GI+F     Q VF+  SG  C 
Sbjct: 121 GAPAVEAFIEKVSRRSNFEFGRARMFGCVGWALCASIVGIMFT-INNQFVFWLGSG--CA 177

Query: 390 MLLFGIFFLSK 400
           ++L  + F +K
Sbjct: 178 LILAVLLFFAK 188


Lambda     K      H
   0.333    0.147    0.471 

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: 550
Number of extensions: 29
Number of successful extensions: 4
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: 415
Length of database: 417
Length adjustment: 31
Effective length of query: 384
Effective length of database: 386
Effective search space:   148224
Effective search space used:   148224
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.5 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:

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