GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Acidovorax sp. GW101-3H11

Align Fructose import permease protein FrcC (characterized)
to candidate Ac3H11_3036 Fructose ABC transporter, permease component FrcC

Query= SwissProt::Q9F9B1
         (360 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_3036
          Length = 319

 Score =  261 bits (667), Expect = 2e-74
 Identities = 142/307 (46%), Positives = 191/307 (62%), Gaps = 6/307 (1%)

Query: 51  PLIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLSVGAIM 110
           P I L+L+  AF      +F SA    LILQQV +V ++   QTLVILTAGIDLS G +M
Sbjct: 16  PFIALILAC-AFFATQSERFLSAQNFALILQQVMVVAVIAIGQTLVILTAGIDLSCGMVM 74

Query: 111 VLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQIVLA 170
            L  ++M +    YG    +++ CG+ V  L G ING LV ++KLPPFIVTLG   I  A
Sbjct: 75  ALGGIVMTKMAADYGLSAPVAIACGMAVTMLFGLINGLLVTKIKLPPFIVTLGTLNIAFA 134

Query: 171 SNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNRTAW 230
           +  LYS  +TI   DI A  + L   G  F++G     +G V+M+ L  + W+ L  TA 
Sbjct: 135 ATQLYSGAQTIT--DIPAGMTAL---GNTFQLGQTAIVWGAVLMLALYLVTWFALRETAP 189

Query: 231 GRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQFANI 290
           GR+VYAVG+ PEA +L G+   ++L+ +Y L+GL   +A    + R G+  P AGQ  N+
Sbjct: 190 GRHVYAVGNSPEATRLTGIATDKVLLGVYVLAGLFYGIASLLSVARTGAGDPNAGQTENL 249

Query: 291 ESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIIIAVA 350
           ++I+AVV+GG SLFGGRG I+G L GALIVGVF  GL LMG    +  L+ G+L+I+AVA
Sbjct: 250 DAISAVVLGGTSLFGGRGVILGTLVGALIVGVFRNGLTLMGVSSVYQILVTGILVILAVA 309

Query: 351 IDQWIRK 357
            DQ  RK
Sbjct: 310 TDQLSRK 316


Lambda     K      H
   0.327    0.141    0.420 

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: 356
Number of extensions: 19
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: 360
Length of database: 319
Length adjustment: 28
Effective length of query: 332
Effective length of database: 291
Effective search space:    96612
Effective search space used:    96612
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 (21.7 bits)
S2: 49 (23.5 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