GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Shew_2731 in Dinoroseobacter shibae DFL-12

Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate 3610175 Dshi_3556 Na+/solute symporter (RefSeq)

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



>FitnessBrowser__Dino:3610175
          Length = 598

 Score =  655 bits (1689), Expect = 0.0
 Identities = 344/601 (57%), Positives = 431/601 (71%), Gaps = 32/601 (5%)

Query: 1   MDVQTLTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFI 60
           MD  TL  ++VG +FALY GIAIW+RAGST EFY AG GV+PV+NGMATAADWMSAASFI
Sbjct: 1   MDQTTLNIIVVGLSFALYFGIAIWARAGSTSEFYAAGRGVNPVVNGMATAADWMSAASFI 60

Query: 61  SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVA 120
           S+AG+++FVGY  S +LMGWTGGYVL+AL +APYLRKFGKFTVP+FIGDR+YS  AR V 
Sbjct: 61  SMAGLIAFVGYSNSSFLMGWTGGYVLMALLLAPYLRKFGKFTVPEFIGDRFYSTKARVVG 120

Query: 121 VVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVA 180
           V+C I I  TY+ GQM G GV FSRFLEV   TG+     VVF YAVLGGMKGITYTQVA
Sbjct: 121 VICLIVISTTYVIGQMTGAGVAFSRFLEVSSTTGLVTASCVVFVYAVLGGMKGITYTQVA 180

Query: 181 QYCVLIFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGN-NTGVYLLEKLDGLSAQLGF 239
           QY VLI A+ +PAIFIS+ +TG+ +P LG  + +  A G    G  LL  LDGL   LGF
Sbjct: 181 QYVVLIIAYTIPAIFISLQLTGNPIPGLGLFSNM--APGQVGAGEPLLVTLDGLLTDLGF 238

Query: 240 SQYTEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTT 299
           + YT GS   +   F T +LM GTAGLPHVI+RFFTVP+V DAR+SAGW LVFIA++Y T
Sbjct: 239 NAYTTGSSPFLMALF-TLSLMIGTAGLPHVIIRFFTVPRVADARISAGWTLVFIALLYLT 297

Query: 300 IPALAAFSRVNMIETI--NGPESTGVAYETAPD-----WIKNWEKTGLIKWDDKNNDGKI 352
            PA+ A +R+N+ + +   G +   V  E   +     W+  W++TGL+ W+DKN DG+I
Sbjct: 298 APAVGAMARLNITDLMWPEGTQGEAVTIEMIQNDPEYAWMNTWQQTGLLGWEDKNGDGRI 357

Query: 353 YY--------------AKGETNEM-KIDRDIMVLATPEIANLPAWVIALVAAGGLAAALS 397
            Y              A  + NE+   +RDI+VLA PEIANLP WVIAL+AAGG+AAALS
Sbjct: 358 QYYNDANPSMTERAEAAGWQGNELTNFNRDILVLANPEIANLPGWVIALIAAGGIAAALS 417

Query: 398 TSAGLLLVISTSVSHDLLKKNFMPDISDKQELLYARIAAALGIVMAGYFGINPPGFVAAV 457
           T+AGLLL IS+++SHDL+K  F P IS+K ELL ARI+ A  IV+A Y G+NPPGF A V
Sbjct: 418 TAAGLLLAISSAISHDLIKTVFNPSISEKGELLAARISMAGAIVVATYLGLNPPGFAAQV 477

Query: 458 VAIAFGLAASSLFPAIIMGIFSRTMNKEGAIAGMVIGLLFSASYIIYFK--FVNPGDN-- 513
           VA+AFGLAA++LFPA++MGIFS+ +N  GA  GM++GL+ + +Y+  +   F  PG N  
Sbjct: 478 VALAFGLAAATLFPALMMGIFSKRINASGATWGMLVGLISTCAYLFTYLGIFFVPGTNFL 537

Query: 514 --NASNWLFGISPEGIGMLGMIINFAVAFIVSKVTAAVPQNVVDMVESIRFPKGAGEAHD 571
              ASN+LFGI P   G +G ++NFAVA +VS+ T   PQ + D+VES+R P+GAG A D
Sbjct: 538 EPTASNYLFGIPPTHFGPIGALLNFAVAILVSRATEEPPQEIQDLVESVRIPRGAGAAVD 597

Query: 572 H 572
           H
Sbjct: 598 H 598


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: 1057
Number of extensions: 33
Number of successful extensions: 6
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: 572
Length of database: 598
Length adjustment: 37
Effective length of query: 535
Effective length of database: 561
Effective search space:   300135
Effective search space used:   300135
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