GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fcbT3 in Sinorhizobium meliloti 1021

Align FcbT3, component of Tripartite 4-chlorobenzoate symporter (also binds and may transport 4-bromo-, 4-iodo-, and 4-fluorobenzoate and with a lower affinity, 3-chlorobenzoate, 2-chlorobenzoate, 4-hydroxybenzoate, 3-hydroxybenzoate, and benzoate) (characterized)
to candidate SMa0151 SMa0151 hypothetical protein

Query= TCDB::Q9RBQ9
         (439 letters)



>FitnessBrowser__Smeli:SMa0151
          Length = 909

 Score =  213 bits (543), Expect = 2e-59
 Identities = 129/426 (30%), Positives = 223/426 (52%), Gaps = 9/426 (2%)

Query: 16  VLLFLGLPVAYSFFAINVVGAWLFLGGDS--ALGQLVRNGLVAVASFSLTPIPLFILMGE 73
           VLL  G+P+A++         ++  G      LG  + +G   +A+ +   IP+F+LMG 
Sbjct: 8   VLLATGMPIAFALGLAAFAALYMQSGAGIFYVLGDTMFSG---IANLAYVSIPMFVLMGA 64

Query: 74  LLFHTGLAQRAIDGIDKVIPRLPGRLAVIAVVAGTFFSAISGSTIATTAMLGSLMLPMML 133
            +  +         +D+ + R+PG L +  + A   FS ++GS+ AT A +G + +P M+
Sbjct: 65  AVASSPAGSDLYTSLDRWLNRIPGGLILSNIGACAIFSGMTGSSPATCAAIGKMGIPEMM 124

Query: 134 ARGYEPKLGMGPIIAIGGVDMLIPPSALAVLLGSLAGISISKLLIGGVLPGLLLAISFVA 193
            RGY   +  G I A G + +LIPPS   ++ G     SI +L + G+LPG+LL I F+ 
Sbjct: 125 RRGYPASVASGSIAAGGTLGILIPPSVTLIVYGIATETSIGRLFMAGILPGILLTIMFMT 184

Query: 194 YIVASAKLRPESAPREELVVLRGWERWRELVVYVLPLSLIFVAIVAVISGGVATPTEAAA 253
           + V   K +      E  +V    +    ++  +LP  LI    + V+ GG+ATP+EAA 
Sbjct: 185 WAVIDCKRK--GYEFEARLVRYSMKERLAVLPRILPFLLIIAGTLYVLYGGIATPSEAAG 242

Query: 254 IGCAATLAITLM-YRALRWQSLVQALQGTVAISGMILFIIVAATTFSQVLSFSGATNGIV 312
            G   TLA+ ++ YR  R++ +       +  S MI+ I+ AA  F+  LS    T  + 
Sbjct: 243 AGAFLTLAVVIVAYRLFRFRPVAGIFGSAMKESVMIMMIMAAAELFAFALSSLFITQTVA 302

Query: 313 DLVQSSGLPPAGVVAIMLAILIFLGLFVDQVSMMLLTLPFYMPIVKSLGIDQIWFGVMYL 372
             +    +    ++A++   L+  G+F+  V+++++T P   PIV   G D  WF ++  
Sbjct: 303 AAIADMEVNRWVLMAVINVFLLICGMFLPPVAVIVMTSPMLFPIVTQAGFDPYWFAIVLT 362

Query: 373 ICMQLGLLMPPHGMLLYTMKGVAPKHITMGQVFASAMPYVGLSFTMLILIFFWPGIATWL 432
           I M++GL+ PP G+ L+ +  +AP+ I    +   ++PYV + F  +IL+  +P +ATWL
Sbjct: 363 INMEVGLITPPIGLNLFVINAIAPQ-IPTKDILWGSLPYVLVMFLAIILLCVFPDVATWL 421

Query: 433 PDVFVG 438
           P+  +G
Sbjct: 422 PNQMLG 427


Lambda     K      H
   0.329    0.143    0.433 

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: 767
Number of extensions: 31
Number of successful extensions: 4
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: 439
Length of database: 909
Length adjustment: 38
Effective length of query: 401
Effective length of database: 871
Effective search space:   349271
Effective search space used:   349271
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: 54 (25.4 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