GapMind for catabolism of small carbon sources

 

Alignments for a candidate for rocE in Lactobacillus oryzae SG293

Align Amino-acid permease RocE (characterized)
to candidate WP_034528194.1 LOSG293_RS05955 amino acid permease

Query= SwissProt::P39137
         (467 letters)



>NCBI__GCF_000740055.1:WP_034528194.1
          Length = 485

 Score =  373 bits (958), Expect = e-108
 Identities = 184/478 (38%), Positives = 295/478 (61%), Gaps = 18/478 (3%)

Query: 4   NQDNGNQLQRTMKSRHLFMISLGGVIGTGFFLGTGFTINQAGPLGAVLSYLVGGFIMFLT 63
           +    +Q++R +K+RH+ MI+LGG IGTG F+ +G  I+ AGP GA+++Y   G +++  
Sbjct: 3   DDQGSHQVKRELKTRHVSMIALGGSIGTGLFVASGSAISTAGPGGALVAYTAMGLMVYFL 62

Query: 64  MLCLGELAVAFPVSGSFQTYATKFISPAFGFAFGWLYWLGWAVTCAIEFLSAGQLMQRWF 123
           M  LGE+A   PVSGSF  YATK++ PA GFA GW YW  WA+T A++  +A  +M+ W 
Sbjct: 63  MTSLGEMATYMPVSGSFAAYATKYVDPAMGFAMGWNYWFNWAITLAVDISTAALVMKFWL 122

Query: 124 PHIDVWIWCLVFAALMFILNAITTKAFAESEFWFSGIKILIILLFIILGGAAMFGLIDLK 183
           P I  WIW ++   ++F+LNA+T KAF ESE+W + IK++ + +F+ +G A +FG++   
Sbjct: 123 PDIPGWIWSVLVLVIIFMLNALTVKAFGESEYWMAMIKVVTVFIFLAVGVATIFGIM--- 179

Query: 184 GGEQAPFLTHFYEDGLFPNGIKAMLITMITVNFAFQGTELIGVAAGESEDPEKTIPRSIK 243
           GG          ++  F  GI  +L   +   F+FQGTEL+G+ AGES+DPEK+IP++I 
Sbjct: 180 GGHATGLENFTRKEAPFVGGIPTILSVFVVAGFSFQGTELVGITAGESKDPEKSIPKAIN 239

Query: 244 QTVWRTLVFFVLSIIVIAGMIPW--------KQAGVVESPFVAVFEQIGIPYAADIMNFV 295
           Q  WR ++F++LSI VIA +IP+          + +  SPF  VF++ G+  AA +MN V
Sbjct: 240 QVFWRIILFYILSIFVIACIIPYTSPQLLGSSASDIAISPFTLVFQRAGLAAAASVMNAV 299

Query: 296 ILIALLSVANSGLYASTRILYAMANEGQAFKALGKTNQRGVPMYSLIVTMAVACLSLLTK 355
           IL +++S ANSG+YAS+R+LY++A +G A KA  KT + GVP+ + I+T  V  L+ +  
Sbjct: 300 ILTSVISAANSGMYASSRMLYSLAVQGYASKAFTKTTRTGVPLNAQIMTTVVGALTFIAS 359

Query: 356 FAQAETVYMVLLSLAGMSAQVGWITISLSQIMFRRKYIREGGKIEDLKFKTPLYPVLPLI 415
            A    +Y+ L++ +G++  + W+ I+LS   FRR +I++G  I +LK+   L+P+ P+ 
Sbjct: 360 IA-GPKIYIWLVAASGLTGFIAWLGIALSHFRFRRAFIKQGHHISELKYHAKLFPIGPIF 418

Query: 416 GLTLNTVVLISLAFDP------EQRIALYCGVPFMIICYIIYHVVIKKRQQANRQLEL 467
            L L  ++++    D       +Q    Y  VP  I  Y  Y +  + +  +  +++L
Sbjct: 419 ALILCLLIIVGQDLDAFTNFNWQQISITYLSVPIFIGLYSYYKIRYRTKLISLEKIDL 476


Lambda     K      H
   0.329    0.142    0.438 

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: 568
Number of extensions: 33
Number of successful extensions: 4
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: 467
Length of database: 485
Length adjustment: 33
Effective length of query: 434
Effective length of database: 452
Effective search space:   196168
Effective search space used:   196168
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 51 (24.3 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