GapMind for catabolism of small carbon sources

 

Alignments for a candidate for frcC in Herbaspirillum seropedicae SmR1

Align Fructose import permease protein FrcC (characterized)
to candidate HSERO_RS05325 HSERO_RS05325 ribose ABC transporter permease

Query= SwissProt::Q9F9B1
         (360 letters)



>FitnessBrowser__HerbieS:HSERO_RS05325
          Length = 328

 Score =  203 bits (517), Expect = 5e-57
 Identities = 116/306 (37%), Positives = 179/306 (58%), Gaps = 9/306 (2%)

Query: 46  SPAAVPLIVLVLSLIAFGVILGGKFFSAFTMTLILQQVAIVGIVGAAQTLVILTAGIDLS 105
           SP A+PL  LV+  +  G +    FF+      +L+QV+IVGI+    + VILT GIDLS
Sbjct: 27  SPLALPLAGLVVVSLLMG-LASDNFFTLSNWFNVLRQVSIVGILAVGMSFVILTGGIDLS 85

Query: 106 VGAIMVLSSVIMGQFTFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMW 165
           VGA M L+  I        G P  L+++CG+G+    G +NG LVA  ++P  IVTL   
Sbjct: 86  VGAAMALAGTISAGLIVNSGLPAPLALLCGVGLATCIGLLNGALVAWGRMPAIIVTLATM 145

Query: 166 QIVLASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVL 225
            +      +YS         IS     + +FG   RIG  +    V++M+++  L W +L
Sbjct: 146 GVARGVGLIYSGG-----YPISGLPGWISWFGVG-RIG--MVPVPVILMLIVYALAWLLL 197

Query: 226 NRTAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAG 285
            RTA+GR+VYA+G +  AA+L+GV  TR+ +++Y +SG    LA   L GR+ S  P AG
Sbjct: 198 QRTAFGRHVYAIGGNEMAARLSGVKTTRIKLAVYAISGFTSGLAAIILTGRLMSGQPNAG 257

Query: 286 QFANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLI 345
               +++I AVV+GG ++ GGRG ++G L GA+++G+ + GL LMG +P    ++ G++I
Sbjct: 258 VGFELDAIAAVVLGGTAIAGGRGLVVGTLIGAVLLGILNNGLNLMGINPYLQDIIRGVII 317

Query: 346 IIAVAI 351
           ++A+ I
Sbjct: 318 LLAIYI 323


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: 396
Number of extensions: 24
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: 328
Length adjustment: 29
Effective length of query: 331
Effective length of database: 299
Effective search space:    98969
Effective search space used:    98969
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