GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Shew_2731 in Dechlorosoma suillum PS

Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate Dsui_0290 Dsui_0290 SSS sodium solute transporter

Query= reanno::PV4:5209923
         (572 letters)



>FitnessBrowser__PS:Dsui_0290
          Length = 582

 Score =  169 bits (427), Expect = 4e-46
 Identities = 149/580 (25%), Positives = 249/580 (42%), Gaps = 69/580 (11%)

Query: 15  FALYIGIAIW------SRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFISLAGIVSF 68
           F  ++   +W      S+  +  +FY AGGG+    NG+A A D+MSAASF+ ++  V  
Sbjct: 42  FGAFVLATLWITKWAASKTKTAADFYTAGGGITGFQNGLAIAGDYMSAASFLGISAAVFA 101

Query: 69  VGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVAVVCAIFIC 128
            GYDG +Y +G+  G+ ++   MA  LR  GKFT  D    R+ +   R +A    + + 
Sbjct: 102 NGYDGLIYSIGFLVGWPIIMFLMAERLRNLGKFTFADVAAYRFQATPIRALAASGTLVVV 161

Query: 129 FTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVAQYCVLI-- 186
             Y+  QM G G +      ++    V +   ++  Y + GGM   T+ Q+ +  +L+  
Sbjct: 162 AFYLIAQMVGAGQLIKLLFGLDYWMAVVLVGILMMVYVLFGGMTATTWVQIIKAVLLLSG 221

Query: 187 -----------FAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSA 235
                      + F   A+F   +     L   G  A+ ++   + T     E +   +A
Sbjct: 222 ASFMVFMVLAKYGFSPEALFADAVRIKTDLAAKGLLAKALETDPSATA----ETVAAAAA 277

Query: 236 QLGFSQYTEGS--KGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFI 293
             G S    GS  K  I       ALMFGTAGLPH+++RFFTVP  K+AR S  WA  +I
Sbjct: 278 AKGQSIMGPGSFIKDPISAISFGMALMFGTAGLPHILMRFFTVPDGKEARKSVFWATTWI 337

Query: 294 AIMYTTIPALAAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIY 353
              Y  +  +  F  +             V   T P+++   +  G++K     N   I+
Sbjct: 338 GYFY-ILTFIIGFGAI-------------VLVGTNPEFL---DAKGVLK--GGGNMAAIH 378

Query: 354 YAKGETNEMKIDRDIMVLATPEIANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHD 413
            A      +                     +  ++A   A  L+  AGL L  +++VSHD
Sbjct: 379 LANAVGGNV--------------------FLGFISAVAFATILAVVAGLTLSGASAVSHD 418

Query: 414 LLKKNFM-PDISDKQELLYARI-AAALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFP 471
           L    F   ++    E+  +++   ALGI+            +A +V++AF +AAS+ FP
Sbjct: 419 LYASVFRHGNVDSATEMRVSKMTTVALGIIAVVLGIAFEKQNIAFMVSLAFAIAASANFP 478

Query: 472 AIIMGIFSRTMNKEGAIAGMVIGLLFSASYIIYFK--FVNPGDNNASNWLFGISPEGIGM 529
            + M +  +    +GA  G  +GL+ +    +  K  +V+   N    + +  SP    M
Sbjct: 479 VLFMSVLWKDCTTKGAFYGGFLGLITAVVLTVLSKSIWVDILGNKTEIFPYA-SPALFSM 537

Query: 530 LGMIINFAVAFIVSKVTAAVPQNVVDMVESIRFPKGAGEA 569
               I   +  ++ +   A  + V  + + IR   G G A
Sbjct: 538 AAGFIGIWLFSLMDRSEQAAKERVAYLDQEIRSETGIGAA 577


Lambda     K      H
   0.326    0.140    0.423 

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: 924
Number of extensions: 53
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 572
Length of database: 582
Length adjustment: 36
Effective length of query: 536
Effective length of database: 546
Effective search space:   292656
Effective search space used:   292656
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: 53 (25.0 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