GapMind for catabolism of small carbon sources

 

Alignments for a candidate for proP in Paraburkholderia bryophila 376MFSha3.1

Align Ectoine/proline transporter ProP (characterized)
to candidate H281DRAFT_02725 H281DRAFT_02725 MFS transporter, MHS family, proline/betaine transporter

Query= SwissProt::Q79VC4
         (504 letters)



>FitnessBrowser__Burk376:H281DRAFT_02725
          Length = 429

 Score =  219 bits (558), Expect = 2e-61
 Identities = 136/420 (32%), Positives = 221/420 (52%), Gaps = 25/420 (5%)

Query: 33  IKGTVVGNFMEWYDFGIYGYLTVTMTAVFTQGLPQEWQLLAVMFGFAVSYLVRPLGGLVL 92
           I  T +GN +E+YD  +YGY   T++ +F     +   LL  +  FA+SYL RP+G LVL
Sbjct: 24  IVATSIGNALEFYDLVVYGYFASTLSRLFFPTHDRTVSLLLTLGTFALSYLARPVGALVL 83

Query: 93  GPLGDKVGRQKVLYVTMAMMAVSTALIGLLPTAASIGAWALVLLYLLKMVQGFSTGGEYA 152
           G   D+ GR+  L +++ +M + T L+ ++P  A+IG  A +L++L +++QGFS GGE+ 
Sbjct: 84  GSYSDRHGRKASLTLSIGLMTLGTGLVAVMPPYATIGIAAPILIFLSRLLQGFSAGGEFG 143

Query: 153 GATTYVAEFAPDRRRGFFGAFLDMGSYLGFAAGASVVAITTW--VTTHFYGATAMEDFGW 210
            +T ++ E AP  R GF      M S+   + GAS +  + +  + T       +E +GW
Sbjct: 144 SSTAFLVEHAP-ARSGF------MSSWQFSSQGASTLLASLFGALLTGLLTPPQLEGWGW 196

Query: 211 RIPFLTAIPLGIIAVYLRTRIPETPAFENNQDEPNAVVEKDTEDPYARLGLAGVIRHHWR 270
           RIPFL  + +G I +Y+R R+ ETP F   +   + V                V+     
Sbjct: 197 RIPFLFGMLIGPIGLYIRRRMDETPEFARAEKLASPV--------------RVVLATQKE 242

Query: 271 PLLIGIAIVAATNTAGYALTSYMPVYLEEQIGLHSASAAAVTVPILVVMSLLLPFVGMWS 330
            +L+ I  +  T TA Y L  YMP Y   Q+ L  +S    T+    +M  L+P VG  S
Sbjct: 243 RVLVSIGSLVLTTTANYMLL-YMPTYATHQLKLSPSSGFIATLVAGFIMMALVPVVGHLS 301

Query: 331 DRVGRKPVYATAVAATLILMVPAFLIMNT-GTIGAVLIALSMVAIPTGLYVALSASALPA 389
           D++GR  +        L+ + PAF++MN   ++  +L  +  VA+    Y A   + +  
Sbjct: 302 DKLGRIRIMLPVGVLFLVTVYPAFMLMNAYPSLPMLLACVIWVALLKATYFAPIPALMAD 361

Query: 390 LFPTASRFSGMGISYNISVSLFGGTTPLITQFLLQKTGLDIVPALYIMFFSAIAGVALLF 449
           LFP  +R +GM  +YNI  ++FGG TP++   L+  T  ++ P LY+M  + I+   L++
Sbjct: 362 LFPVETRTTGMAFAYNIGTTIFGGFTPVVVAALIAFTHNNLAPGLYLMIAAVISLFTLMW 421


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: 45
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: 429
Length adjustment: 33
Effective length of query: 471
Effective length of database: 396
Effective search space:   186516
Effective search space used:   186516
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