GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuF in Sinorhizobium fredii NGR234

Align Trehalose/maltose transport system permease protein MalF (characterized)
to candidate WP_015888140.1 NGR_RS09950 sugar ABC transporter permease

Query= SwissProt::O51924
         (295 letters)



>NCBI__GCF_000018545.1:WP_015888140.1
          Length = 307

 Score =  213 bits (542), Expect = 4e-60
 Identities = 111/281 (39%), Positives = 179/281 (63%), Gaps = 4/281 (1%)

Query: 11  YREAKLGYLMILPLLTVVLVFIILPVMGTFWISLHRDVTFIPEKP--FVGLRNYLRVLSA 68
           + E  L YLM+ P + ++L   I P +  F+ ++HR ++  P+ P  FVG+ N+ R+LS 
Sbjct: 22  WAERHLRYLMLAPTVLILLALTIFPSIYMFYAAVHR-ISPNPDLPWEFVGVGNFARLLSD 80

Query: 69  REFWYSTFVTVSFSFVSVSLETILGLSFALILNERLKGRGVLRAIVLIPWAVPTIISART 128
            +F  +   TV F+ V+V+LE +LGL  AL+L+  ++    L+ +++IP  +P I  A T
Sbjct: 81  PQFHVALRNTVVFTLVAVALEFLLGLGLALLLDRFIRRLSFLKTVLMIPMMLPPIAVAIT 140

Query: 129 WELMYNYSYGLFNWILSILGVSPVNWLGTPISAFFAIVIADVWKTTPFMTLLLLAGLQAI 188
           W+L+Y   +G+ N I+ +LG+    W G    A F+I++ADVW+ TPF+ LL+LAGL ++
Sbjct: 141 WKLIYEPQFGVLNEIMFLLGLPVQAWAGDVNLAMFSIIVADVWQWTPFVFLLMLAGLASL 200

Query: 189 PQDLYEAALIDGASMFERFKSITLPLLKPVLIVALILRTIDALRVFDIIYVLTGGGPGGA 248
           P + YEAA +DGAS + +F  +TLP LKPV+ +AL+LR +DALR+FD++++LTGGGP   
Sbjct: 201 PVEPYEAAALDGASSWRQFWDLTLPFLKPVIAIALLLRVMDALRLFDLVFILTGGGPADR 260

Query: 249 TTSISLLAFNY-YNLGDYGIGSAISILTFVLVLSFTIVYLK 288
           T  +SL  +   Y   D G  +AIS+    + +  +  ++K
Sbjct: 261 TKVLSLYIYQVAYRFADPGYAAAISLFVLFVTIVLSTWFMK 301


Lambda     K      H
   0.329    0.145    0.439 

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: 275
Number of extensions: 12
Number of successful extensions: 2
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: 295
Length of database: 307
Length adjustment: 27
Effective length of query: 268
Effective length of database: 280
Effective search space:    75040
Effective search space used:    75040
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 Apr 09 2024. 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