GapMind for catabolism of small carbon sources

 

Alignments for a candidate for Shew_2731 in Leeuwenhoekiella blandensis MED217

Align actP-like component of L-lactate and L-malate uptake system (characterized)
to candidate WP_009781829.1 MED217_RS17145 cation acetate symporter

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



>NCBI__GCF_000152985.1:WP_009781829.1
          Length = 590

 Score =  766 bits (1979), Expect = 0.0
 Identities = 391/601 (65%), Positives = 459/601 (76%), Gaps = 40/601 (6%)

Query: 1   MDVQTLTYLIVGFTFALYIGIAIWSRAGSTKEFYVAGGGVHPVMNGMATAADWMSAASFI 60
           M VQ  T+++VG TFALY GIAIW+RAGSTKEFYVAGGGV P+ NGMATAADWMSAASFI
Sbjct: 1   MSVQLWTWILVGITFALYFGIAIWARAGSTKEFYVAGGGVSPLANGMATAADWMSAASFI 60

Query: 61  SLAGIVSFVGYDGSVYLMGWTGGYVLLALCMAPYLRKFGKFTVPDFIGDRYYSQAARTVA 120
           S+AGI+SF GYDGSVYLMGWTGGYVLLAL +APYLRKFGKFTVPDFIGDRYYS  ARTVA
Sbjct: 61  SMAGIISFAGYDGSVYLMGWTGGYVLLALLLAPYLRKFGKFTVPDFIGDRYYSNTARTVA 120

Query: 121 VVCAIFICFTYIAGQMRGVGVVFSRFLEVEVDTGVYIGMAVVFFYAVLGGMKGITYTQVA 180
           V+CA+ + FTY+AGQMRGVG+VFS+FL+VE+ TGV IGMAVV  +A LGGMKGITYTQVA
Sbjct: 121 VICALIVSFTYVAGQMRGVGIVFSQFLQVEITTGVIIGMAVVLVFAFLGGMKGITYTQVA 180

Query: 181 QYCVLIFAFMVPAIFISVMMTGHILPQLGFGAELVDAAGNNTGVYLLEKLDGLSAQLGFS 240
           QYCVLIFAFMVPAIFIS+ MTG+I+PQ+G G  + D      G +LLEKLD L  QLGF 
Sbjct: 181 QYCVLIFAFMVPAIFISIQMTGNIIPQIGMGGRVED------GTFLLEKLDNLHTQLGFK 234

Query: 241 QYTEGSKGMIDVFFITGALMFGTAGLPHVIVRFFTVPKVKDARVSAGWALVFIAIMYTTI 300
           +YTEG+K   DVF IT ALM GTAGLPHVIVRFFTVP VKDAR SAG AL+ IAI+YTT 
Sbjct: 235 EYTEGTKSTWDVFAITLALMAGTAGLPHVIVRFFTVPNVKDARKSAGLALLLIAILYTTA 294

Query: 301 PALAAFSRVNMIETINGPESTGVAYETAPDWIKNWEKTGLIKWDDKNNDGKIYYAKG--- 357
           PA++ F+R N+IET++  E     Y + P+W KNWE  GLI W DKN DGKI Y  G   
Sbjct: 295 PAVSVFARTNLIETVSNQE-----YASLPEWFKNWENMGLIAWSDKNKDGKIQYVNGDAT 349

Query: 358 -----------------------ETNEMKIDRDIMVLATPEIANLPAWVIALVAAGGLAA 394
                                  ETNE+ +DRDIMVLA PEIA LP+WVIALVAAGGLAA
Sbjct: 350 TGKPEFTEARGTNGERIITNTSTETNELYVDRDIMVLANPEIAQLPSWVIALVAAGGLAA 409

Query: 395 ALSTSAGLLLVISTSVSHDLLKKNFMPDISDKQELLYARIAAALGIVMAGYFGINPPGFV 454
           ALST+AGLLLVISTSVSHDL+KK   P+IS+K ELL AR++  + I++AG FGI PPGFV
Sbjct: 410 ALSTAAGLLLVISTSVSHDLIKKQLKPNISEKGELLAARLSILVAIIVAGLFGIYPPGFV 469

Query: 455 AAVVAIAFGLAASSLFPAIIMGIFSRTMNKEGAIAGMVIGLLFSASYIIYFKFVNPG--- 511
           AAVVA+AFGLAA+S FPAI++GIF + MNK+GAI+GM++G L    Y+I FK    G   
Sbjct: 470 AAVVALAFGLAAASFFPAIVLGIFDKRMNKQGAISGMIVGTLLMLFYMIRFKTGLIGVLE 529

Query: 512 DNNASNWLFGISPEGIGMLGMIINFAVAFIVSKVTAAVPQNVVDMVESIRFPKGAGEAHD 571
              AS W FG SPEG G   M++N  ++  +S++T A P++V ++VE IR P GAGEA  
Sbjct: 530 PLPASEWWFGTSPEGFGTFAMLVNVVISVTISRLTPAPPEDVQEIVERIRIPSGAGEAQS 589

Query: 572 H 572
           H
Sbjct: 590 H 590


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: 1090
Number of extensions: 56
Number of successful extensions: 5
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: 590
Length adjustment: 36
Effective length of query: 536
Effective length of database: 554
Effective search space:   296944
Effective search space used:   296944
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 24 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