GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__SB2B:6936677
          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 (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