GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treEIIA in Stenotrophomonas chelatiphaga DSM 21508

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate WP_057508246.1 ABB28_RS08640 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::WCS417:GFF4500
         (838 letters)



>NCBI__GCF_001431535.1:WP_057508246.1
          Length = 585

 Score =  277 bits (708), Expect = 1e-78
 Identities = 191/563 (33%), Positives = 280/563 (49%), Gaps = 16/563 (2%)

Query: 270 LLRGVCASPGSAFGQVVQVTDPELVITEQGTGGATERAALTR---GLLAANEALQVLQDK 326
           LL G  AS G+A G+        L + EQ          L R    L AA   +  L+ +
Sbjct: 18  LLSGHGASRGTALGRARVRLAHALEVAEQRVAPQQVDKELKRLHVALDAARNEMHDLRQR 77

Query: 327 AAGSAQ---AEIFRAHQELLEDPTLLEHAHRLLGEGK-SAAFAWNSATLATVTLFQGLGN 382
             G+      E    H  LL+DP LL     L+  G  SA +A          +F G+ +
Sbjct: 78  LQGALNQEAGEFLDLHALLLDDPELLFGLDELIRSGPYSAGYALRLQRDRLAKVFDGMDD 137

Query: 383 ALIAERAADLADVGQRVLKLILGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFVT 442
           A +  R  DL  V  R+   +  +   A       IL+ + + PS+ A L ++ V+  VT
Sbjct: 138 AYLKSRMDDLDHVIGRIHAFLQPVLPPAVKGLAGEILVCDNIAPSEMAQLQSQGVVAIVT 197

Query: 443 VAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLEA 502
            AG A SH AILAR+L LP I  VP  +  +++G  +++D   G + + P    +     
Sbjct: 198 TAGSALSHSAILARSLHLPLIVNVPGLLHKVSDGDVLIVDGSDGSITVNPQAENLRDYRV 257

Query: 503 ARKHQVLRHQRDVAQA-SLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFL 561
             K    R QR++ +  S P+ TRD   + + AN  SL++V  A   G +G+GL R+EFL
Sbjct: 258 RLKEHA-REQRELGRLRSKPSRTRDQVDIALLANAESLEDVTQAHAFGAQGLGLYRTEFL 316

Query: 562 YLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDK-PLAYVPMDAETNPFLGLR 620
           +L RN  P  EEQ  TY   A  +   R + +RTLD+G DK     + +  E NP LGLR
Sbjct: 317 FLQRNELPDEEEQFHTYRDAALGM-AGRLVTIRTLDLGADKADRTGLTLSNEENPALGLR 375

Query: 621 GIRLCLERPQLLREQFRAILASAGFARLHIMLPMVSLLSEL-----HLARKILEEEALAL 675
           G+RL L RP +   Q RAIL ++ + ++ I++PMVS   EL      + R   +  A   
Sbjct: 376 GVRLSLARPLVADTQLRAILRASAYGKVRILIPMVSTREELLAVRRRMTRLTAQLRAEGH 435

Query: 676 GLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFH 735
            ++E   LG MIEVP+AA   + F   VDF SIGTNDL QY LA DR++  L       H
Sbjct: 436 AVSERVPLGAMIEVPAAAFALESFIDLVDFLSIGTNDLVQYLLAADRNNEALGELYSPLH 495

Query: 736 PAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVR 795
           PAVLRL+   ++    H   V VCG +A +A   P+L+ LG+ E S+    +  ++  +R
Sbjct: 496 PAVLRLLKLVIETGQRHQIPVAVCGEIAGDARLAPLLLALGLTEFSLHPGTLLEVRRAIR 555

Query: 796 ELDLADCQIIARQVLGLEEAAEV 818
           E DL + +  A ++L   +   +
Sbjct: 556 ESDLGELRARAPKLLAARDRRSI 578


Lambda     K      H
   0.318    0.133    0.371 

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: 1000
Number of extensions: 53
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: 838
Length of database: 585
Length adjustment: 39
Effective length of query: 799
Effective length of database: 546
Effective search space:   436254
Effective search space used:   436254
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: 54 (25.4 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