GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lacF in Sinorhizobium meliloti 1021

Align LacF, component of Lactose porter (characterized)
to candidate SM_b20232 SM_b20232 sugar ABC transporter permease

Query= TCDB::P29823
         (298 letters)



>FitnessBrowser__Smeli:SM_b20232
          Length = 314

 Score =  165 bits (418), Expect = 1e-45
 Identities = 103/299 (34%), Positives = 166/299 (55%), Gaps = 11/299 (3%)

Query: 2   ATTSRSSLKRYYDVNGWLFVAPAIALISVFMLYPILRSLVLSLYTGRGMM-LKFSGTGNL 60
           A  +R S K    + G+LFV P    + +F+  P+  SLVLS++   G     F G  N 
Sbjct: 14  AGRTRLSAKHREWIAGYLFVLPDALGLFIFLGVPMALSLVLSVFEVNGFGGYSFVGARNY 73

Query: 61  VRLWNDPVFWQALQNTVIFFVVQVPIMITMALILAAMLNNPKLRYSGLFRTMIFLPCVSS 120
           +R+WNDP+FW+  + T ++  + VP++    L LA ++     R++ + R+M F P + S
Sbjct: 74  LRMWNDPLFWKGARVTALYAAMLVPLLYVCGLGLALLVQRTD-RFNAIMRSMFFAPHMVS 132

Query: 121 LVAYSILFKSMF-SLDGVVNNTLLAIGIIGEPIGWLTDPFWAKVLIIIAITWRWTGYNMI 179
           LV  +++++ M     GVV+    A+ I G  I  L DP +A + I++   W   G+ M+
Sbjct: 133 LVVVALVWQFMVVDKIGVVSRLTAALDIGG--ISLLGDPNFALITIVLVSVWFLMGFYML 190

Query: 180 FYLAALQNIDRSIYEAAKIDGVPSWGRFAFLTIPMLKPVILFTTITSTIGTL---QLFDE 236
            +L  LQ+I R  YEAA IDG  +  RF F+T+P+LKP   F  + S +  +   Q FD 
Sbjct: 191 IFLGGLQDIPRQYYEAAMIDGAGAIARFWFITLPLLKPTSFFVIMVSMVAAVAGAQAFDI 250

Query: 237 VYNFTEGTGGPANSTLTLSLYIYNLTFRFMPSFSYAATVSYVIVLMVAVLSFLQFYAAR 295
           +Y  T+  GGPAN+T  L +YIY   F F  +F YAA ++ ++V+ + +++ + F   R
Sbjct: 251 IYVMTK--GGPANATSVLIVYIYQQAFGF-GAFGYAAAMASILVVALMIVTAVFFALTR 306


Lambda     K      H
   0.329    0.141    0.435 

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: 252
Number of extensions: 17
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: 298
Length of database: 314
Length adjustment: 27
Effective length of query: 271
Effective length of database: 287
Effective search space:    77777
Effective search space used:    77777
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: 48 (23.1 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