Alignments for a candidate for Shew_2731 in Leeuwenhoekiella blandensis MED217

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources