GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Sinorhizobium meliloti 1021

Align MalF, component of Maltose/trehalose porter (characterized)
to candidate SM_b21220 SM_b21220 sugar ABC transporter permease

Query= TCDB::O51924
         (300 letters)



>FitnessBrowser__Smeli:SM_b21220
          Length = 293

 Score =  211 bits (538), Expect = 1e-59
 Identities = 108/272 (39%), Positives = 174/272 (63%), Gaps = 3/272 (1%)

Query: 23  YLMILPLLTVVLVFIILPVMGTFWISLHRDVTFIPEKPFVGLRNYLRVLSAREFWYSTFV 82
           +L++LPLL V+   I  P++ T  +S         E  FVG  NY+++L    F  +   
Sbjct: 11  WLLMLPLLVVMTAVIGWPLVDTVRLSFTDAKLVGTEGGFVGTANYIKMLGGSNFQRALVT 70

Query: 83  TVSFSFVSVSLETILGLSFALILNERLKGRGVLRAIVLIPWAVPTIISARTWELMYNYSY 142
           T  F+ +SV+ E +LG+  AL+LN++ +GR  LRA++++PWA+PT+++A  W L+YN  Y
Sbjct: 71  TTWFAVISVAAEMVLGVLAALLLNQQFRGRTALRALMILPWALPTVVNATLWRLIYNPEY 130

Query: 143 GLFNWILSILGV--SPVNWLGTPISAFFAIVIADVWKTTPLMTLLLLAGLQAIPQDLYEA 200
           G  N  L+ LG+  S  +WLG P +A  A+++AD WK  PL+ L+ LA LQA+P+D+  A
Sbjct: 131 GALNAALTQLGLLDSYRSWLGEPGTALAALIVADCWKNFPLVALIALAALQAVPRDITAA 190

Query: 201 ALIDGASMFERFKSITLPLLKPVLIVALILRTIDALRVFDIIYVLTGGGPGGATTSISLL 260
           +L+DGA  F RF+ + +P L   L+VAL+LRTI+A +VFDII+V+T GGP  +T ++S+L
Sbjct: 191 SLVDGAGPFNRFRFVIMPYLAGPLLVALVLRTIEAFKVFDIIWVMTRGGPANSTRTLSIL 250

Query: 261 AF-NYYNLGDYGIGSAISILTFVLVLSFTIVY 291
            +   ++    G G++++++  +LV      Y
Sbjct: 251 VYQEAFSFQRAGSGASLALIVTLLVTILAAAY 282


Lambda     K      H
   0.329    0.145    0.436 

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: 290
Number of extensions: 11
Number of successful extensions: 3
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: 300
Length of database: 293
Length adjustment: 26
Effective length of query: 274
Effective length of database: 267
Effective search space:    73158
Effective search space used:    73158
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