GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Shew_2731 in Cupriavidus basilensis 4G11

Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate RR42_RS13875 RR42_RS13875 sodium:solute symporter

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



>FitnessBrowser__Cup4G11:RR42_RS13875
          Length = 683

 Score =  194 bits (492), Expect = 1e-53
 Identities = 100/219 (45%), Positives = 136/219 (62%), Gaps = 6/219 (2%)

Query: 2   DVQTLTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFIS 61
           D   L Y+ +  T A+Y  I +  R     E+YVAG  V  + NGMA AADWMSAASFI 
Sbjct: 39  DALWLGYVFLFVTIAIYACIGLICRTSDLNEYYVAGRRVPALFNGMAIAADWMSAASFIG 98

Query: 62  LAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRY------YSQA 115
           LAGI+   GY+G  Y+MGWTGGY L+A  +APYLRK+G +T+PDF+  RY       +  
Sbjct: 99  LAGILFASGYEGLAYVMGWTGGYCLVAFLLAPYLRKYGGYTIPDFLAARYGNGKPGGNMP 158

Query: 116 ARTVAVVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGIT 175
            R +AV+ A    F Y+  Q++GVG++ +RF+ VE   GV+ G+A +   + LGGM+ +T
Sbjct: 159 VRAIAVMAASLCSFVYLVAQIQGVGLIVTRFIGVEFAVGVFFGLAGILVCSFLGGMRAVT 218

Query: 176 YTQVAQYCVLIFAFMVPAIFISVMMTGHILPQLGFGAEL 214
           +TQVAQY +LI AF+V    I+       LPQL +G  L
Sbjct: 219 WTQVAQYIMLIAAFLVTVSMIAWKHHHEALPQLSYGTLL 257



 Score =  184 bits (467), Expect = 1e-50
 Identities = 113/291 (38%), Positives = 156/291 (53%), Gaps = 13/291 (4%)

Query: 259 LMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTIPALAAFSRVNMIETINGP 318
           LM GTA LPH++ R +T P VK++R S  WA+ FIA++Y + PALAA  +    + +   
Sbjct: 386 LMLGTASLPHILTRLYTTPSVKESRNSVAWAVFFIALLYVSAPALAALVKYEFFQHL--- 442

Query: 319 ESTGVAYETAPDWIKNWEKTG--LIKWDDKNNDGKIYYAKGETNEMKIDRDIMVLATPEI 376
              G  Y   P W+  W K    +    D N DG + +A     E+ I  D++VLA PEI
Sbjct: 443 --VGTPYAELPQWVVQWRKVDPPVFGIRDVNGDGIVQWA-----EILIQPDMIVLAAPEI 495

Query: 377 ANLPAWVIALVAAGGLAAALSTSAGLLLVISTSVSHDLLKKNFMPDISDKQELLYARIAA 436
           A LP  +  LVAAG LAAALST+ GLLL I+ ++SHD+         S ++ +  A+I  
Sbjct: 496 AGLPYVISGLVAAGALAAALSTADGLLLTIANALSHDVFYHMGDRTASHQRRVTTAKIVL 555

Query: 437 ALGIVMAGYFGINPPGFVAAVVAIAFGLAASSLFPAIIMGIFSRTMNKEGAIAGMVIGLL 496
               + A Y     PG +  +V  AF LAASS FP +++ IF R     GA+AGMV GL 
Sbjct: 556 LGVALFASYVTSLRPGNILFLVGAAFSLAASSFFPVLVLAIFWRRTTAAGAVAGMVAGLG 615

Query: 497 FSASYI-IYFKFVNPGDNNASNWLFGISPEGIGMLGMIINFAVAFIVSKVT 546
            +  YI + + F         N  FG+ P   G  G+   FAVA +VS +T
Sbjct: 616 VAVYYIFVNYPFFTRMTGIFGNRWFGVDPIASGAFGVPAGFAVAILVSLLT 666


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: 1058
Number of extensions: 67
Number of successful extensions: 8
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: 683
Length adjustment: 37
Effective length of query: 535
Effective length of database: 646
Effective search space:   345610
Effective search space used:   345610
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: 54 (25.4 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