GapMind for catabolism of small carbon sources

 

Aligments for a candidate for treEIIA in Shewanella amazonensis SB2B

Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate 6936677 Sama_0864 phosphoenolpyruvate-protein phosphotransferase PtsP (RefSeq)

Query= reanno::pseudo3_N2E3:AO353_15995
         (844 letters)



>lcl|FitnessBrowser__SB2B:6936677 Sama_0864
           phosphoenolpyruvate-protein phosphotransferase PtsP
           (RefSeq)
          Length = 744

 Score =  305 bits (780), Expect = 8e-87
 Identities = 203/563 (36%), Positives = 301/563 (53%), Gaps = 15/563 (2%)

Query: 276 LLRGVCASAGSAFGYVVQVA-ERTLEMPEFAA-DQQLERESLERALMHATQALQRLR--- 330
           L  G  AS G A  + + +  E +LE PE  A D   E   L  A+  +  AL  L    
Sbjct: 169 LFTGTSASTGVAIAHALVIGGEISLEQPEACATDVDAEVNRLRLAMGRSRDALTALAQKF 228

Query: 331 DNAAGEAQADIFKAHQELLEDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTL 390
           +N   +  + IF + Q LLED SL  + Q  +  G SA  A +  +      F+++    
Sbjct: 229 ENDHDDELSSIFTSLQSLLEDASLGGEYQREVLAGWSAETAVSRVSLRYVAQFETMEDAY 288

Query: 391 LAERALDLMDVGQRVLKLILGVPDGVWELPDQ-AILIAEQLTPSQTAALDTGKVLGFATV 449
           L ERA D+ D+GQRVL+ ++  P  +   PD+  IL+  +   S  A     K+ G  T 
Sbjct: 289 LRERASDIRDLGQRVLRQLIE-PGRMMLDPDKPVILVTREADTSMLAEFPRQKLAGIVTE 347

Query: 450 GGGATSHVAILARALGLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAK 509
            GG  SH AILARALG+PA+ G+   + +      ++L+A +G L + P+ +V+++    
Sbjct: 348 AGGVNSHAAILARALGVPAIMGVEQVLQANLDKQLLVLNASRGILMVSPSPTVVDEYRNL 407

Query: 510 RQQQRQRHQHELENAARAAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQ 569
              Q+   +   E     A+T DGH   +  N   ++     ++ GA+G+GL R+E  + 
Sbjct: 408 ISAQKALDRQYAEELKEPALTLDGHRIHLYLNAGLMSGVSSEIADGADGVGLYRTEIPFM 467

Query: 570 QRSVAPSHDEQAGTYSAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIR 629
            +   PS  EQ   Y ++ ++    R +V+RTLDVGGDKPL Y P+ SE NPFLG RGIR
Sbjct: 468 LQQRFPSESEQIKVYRSVLQSAAG-RPVVMRTLDVGGDKPLPYFPI-SEENPFLGWRGIR 525

Query: 630 LCLERPQLLREQFRAILSSAG-LARLHIMLPMVSQLSELRLARLMLEEEALALGLRELPK 688
           L L+ P+L   Q RA+L +AG    L I+LPMVS L E+  A L L++    L     P 
Sbjct: 526 LSLDHPELFLVQLRAMLQAAGDTDNLKILLPMVSSLDEIDEALLYLDQAFSELRADVNPS 585

Query: 689 L-----GIMIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPS 743
           L     G+M+EVPA        A  V+F S+G+NDLTQY LA+DR++PR++S  DS+HP 
Sbjct: 586 LARPPVGVMLEVPALLYQLREVAQRVEFVSVGSNDLTQYLLAVDRNNPRVSSLYDSYHPG 645

Query: 744 VLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREV 803
           VLR +   ++    H   V VCG LA E +   LL+ +G DELS++   +  I   +R V
Sbjct: 646 VLRALQLALQECRQHKLDVSVCGELAGEPMGALLLVAMGYDELSMNQGSLAKINYLLRRV 705

Query: 804 ELSDCQAIAHQVLGLESAEQVRE 826
           E S+ + +   V+ + + + VRE
Sbjct: 706 ERSELEQLLALVMQMSNGQDVRE 728


Lambda     K      H
   0.318    0.132    0.370 

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: 1170
Number of extensions: 51
Number of successful extensions: 6
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: 844
Length of database: 744
Length adjustment: 41
Effective length of query: 803
Effective length of database: 703
Effective search space:   564509
Effective search space used:   564509
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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