GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proP in Herbaspirillum seropedicae SmR1

Align Ectoine/proline transporter ProP (characterized)
to candidate HSERO_RS15670 HSERO_RS15670 major facilitator transporter

Query= SwissProt::Q79VC4
         (504 letters)



>FitnessBrowser__HerbieS:HSERO_RS15670
          Length = 427

 Score =  214 bits (544), Expect = 6e-60
 Identities = 132/420 (31%), Positives = 220/420 (52%), Gaps = 20/420 (4%)

Query: 30  RPAIKGTVVGNFMEWYDFGIYGYLTVTMTAVFTQGLPQEWQLLAVMFGFAVSYLVRPLGG 89
           R AI  + +GN +EW+D  IYG   V +   F         LL     F VS+ +RPLG 
Sbjct: 18  RRAIISSSIGNALEWFDILIYGAFAVVIAKQFFPTGDDSVSLLLTFATFGVSFFMRPLGA 77

Query: 90  LVLGPLGDKVGRQKVLYVTMAMMAVSTALIGLLPTAASIGAWALVLLYLLKMVQGFSTGG 149
           +VLG   D+ GR+  L +++ +M V TA+I  +P+ ASIG  A   + L KM+QGFS GG
Sbjct: 78  VVLGAYSDRAGRKAALMLSIMLMTVGTAMIAFMPSYASIGLLAPAGIALGKMIQGFSAGG 137

Query: 150 EYAGATTYVAEFAPDRRRGFFGAFLDMGSYLGFAAGASVVAITTWVTTHFYGATAMEDFG 209
           E+  +T ++ E AP  RRGFF ++      +     A   A+   + T       +  +G
Sbjct: 138 EFGSSTAFLVEHAP-HRRGFFSSWQVASQGISLLLAALFGAVLNNMLT----PEQLASWG 192

Query: 210 WRIPFLTAIPLGIIAVYLRTRIPETPAFENNQDEPNAVVEKDTEDPYARLGLAGVIRHHW 269
           WR+PF+  + +    +Y+R  + E P F+ + ++ NA + +DT              H  
Sbjct: 193 WRVPFIFGLLIAPAGIYIRRHLDEAPEFKESSEKTNAPL-RDT------------FAHQK 239

Query: 270 RPLLIGIAIVAATNTAGYALTSYMPVYLEEQIGLHSASAAAVTVPILVVMSLLLPFVGMW 329
             LLIG   V     + Y L+ Y+P Y  +Q+GL + S+ A      ++M +  P VG  
Sbjct: 240 MRLLIGAGSVIMATVSVY-LSLYIPTYAVKQLGLPAWSSFAAMSVAGLIMFIGSPLVGAL 298

Query: 330 SDRVGRKPVYATAVAATLILMVPAFLIM-NTGTIGAVLIALSMVAIPTGLYVALSASALP 388
           SD++GR P   T+ A  ++L  P F+ + N+     +L+  +++ +   +Y A   + L 
Sbjct: 299 SDKIGRTPFMITSSALYIVLTYPMFVFLTNSPGFLQLLLLQTVIGVLMTMYFAAMPALLA 358

Query: 389 ALFPTASRFSGMGISYNISVSLFGGTTPLITQFLLQKTGLDIVPALYIMFFSAIAGVALL 448
            +FP A+R +GM ++YNI+V++FGG   LI  +L+  TG  +  + +++F + ++ +A L
Sbjct: 359 DIFPVATRGTGMSLAYNIAVTIFGGFAGLIITWLIDFTGDKLSVSYFVIFGAVLSLIASL 418


Lambda     K      H
   0.322    0.138    0.407 

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: 581
Number of extensions: 35
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: 504
Length of database: 427
Length adjustment: 33
Effective length of query: 471
Effective length of database: 394
Effective search space:   185574
Effective search space used:   185574
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 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