GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Cup4G11:RR42_RS13875 RR42_RS13875 sodium:solute
           symporter
          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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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