GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruF in Herbaspirillum seropedicae SmR1

Align Fructose import permease protein FruF (characterized)
to candidate HSERO_RS05180 HSERO_RS05180 sugar ABC transporter permease

Query= SwissProt::Q8G846
         (356 letters)



>FitnessBrowser__HerbieS:HSERO_RS05180
          Length = 359

 Score =  220 bits (561), Expect = 4e-62
 Identities = 131/349 (37%), Positives = 199/349 (57%), Gaps = 21/349 (6%)

Query: 3   EKAKAEGNNFVKKLLSSNLTWSIVAFILLVIICTIFQHDFLALSWNSNTGGLAGPLITML 62
           + A + G+  +  LL   L   + A  +L++I  +    F  L      G L G LI ++
Sbjct: 12  DTAASAGSPMLAGLLRHPLVRPLGALAVLLLIDFLLVPGFFKLEIKD--GHLYGALIDII 69

Query: 63  QESARYLMIATGMTLVISTAGIDLSVGSVMAVAGAAAM--------------QTLSNGMN 108
             +A  ++ A GMTLVI+T G+D+SVG+V+A++GA A               Q +SN   
Sbjct: 70  NRAAPLMLAALGMTLVIATRGVDISVGAVVAISGAVAAILIGGKMVVVDGVSQYVSNVPM 129

Query: 109 VWLSILIALAVGLAIGCVNGALVSFLGLQPFITTLIMMLAGRGMAKVITSGENTDASAVA 168
           VW ++  A+   L  G  NG LV+ LGLQP I TLI+M+AGRG+A+++T G+        
Sbjct: 130 VW-ALCAAMGAALLCGAWNGLLVAGLGLQPIIATLILMVAGRGLAQLLTDGQ----IVTV 184

Query: 169 GNEPLKWFANGFILGIPANFVIAVIIVILVGLLCRKTAMGMMIEAVGINQEASRMTGIKP 228
             +P  +   G++ G+P +  IA  + +L+ LL +KTA+G+ IE+VGIN  ASR+ GI+ 
Sbjct: 185 YYKPFFFLGGGYLFGLPFSLYIAAAMFVLLALLMKKTALGLFIESVGINPVASRLAGIRT 244

Query: 229 KKILFLVYAISGFLAAIAGLFATASVMRVDVVKTGQDLEMYAILAVVIGGTSLLGGKFSL 288
             ++F VY      A +AGL   +++   D    G  LE+ AILAV +GGTSL GGKFSL
Sbjct: 245 AALIFFVYMFCSACAGLAGLMIASNIKSADANNAGLLLELDAILAVTLGGTSLAGGKFSL 304

Query: 289 AGSAVGAVIIAMIRKTIITLGVNAEATPAFFAVVVIVICVMQAPKIHNL 337
            GS +GA+II  +  TI +LGV  E      ++VV ++C+ Q+P+   +
Sbjct: 305 VGSVIGALIIQTLTYTIYSLGVPPEVNMVVKSIVVFLVCLSQSPQFRRM 353


Lambda     K      H
   0.325    0.136    0.384 

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: 333
Number of extensions: 17
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: 356
Length of database: 359
Length adjustment: 29
Effective length of query: 327
Effective length of database: 330
Effective search space:   107910
Effective search space used:   107910
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 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