GapMind for catabolism of small carbon sources

 

Alignments for a candidate for treEIIA in Rhodococcus qingshengii djl-6-2

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate WP_050655247.1 C1M55_RS19650 phosphoenolpyruvate--protein phosphotransferase

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



>NCBI__GCF_002893965.1:WP_050655247.1
          Length = 557

 Score =  298 bits (762), Expect = 7e-85
 Identities = 216/568 (38%), Positives = 295/568 (51%), Gaps = 28/568 (4%)

Query: 264 TQSSATLLRGVCASPGSAFGQVVQVTDPELVITEQGTGGATERAALTRGLLAANEALQVL 323
           T S    + G+  S GS     ++ + PE         G+ E       L+   EAL  +
Sbjct: 2   TASVDNRIAGIGVSAGSVCAPWLRFSTPEPTSAADPITGSPEAE-----LIRIREALDAV 56

Query: 324 QDKAAGSAQ------AEIFRAHQELLEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLF 377
            ++    A+      AEI      +  D  +++ A   L  G   A A   A  A     
Sbjct: 57  AEELLSRAKTVEGVSAEILTTSAAMARDAGIVKAAKANLESGLPTAHAVAVAFDAFCEKL 116

Query: 378 QGLGNALIAERAADLADVGQRVLKLILGIQDSAWDLPERA-ILIAEQLTPSQTASLDTRK 436
             LG  + AERA DL D+GQR + ++ G        P    IL+A  L P+ TA+L T  
Sbjct: 117 TALGGYM-AERATDLRDLGQRAVAVLRGEPMPGIPAPGYPYILVARDLAPADTATLGTSD 175

Query: 437 VLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAE 496
           V+G +T  GG TSH AILA++LG+PA+       L LA GK ++LD   G + ++P+ AE
Sbjct: 176 VVGLLTAEGGPTSHTAILAKSLGIPAVVNCSGTDL-LAEGKLLILDGTTGTVTIDPS-AE 233

Query: 497 IEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLL 556
           + +        V       A A  P  TRDG  V ++AN+ +L++   A     EGVGL 
Sbjct: 234 MRERAVLEASFVAEQS---ASAQGPGRTRDGFAVRLSANIGTLEDAARAGAADCEGVGLF 290

Query: 557 RSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPF 616
           R+EF YL R+ APS EEQA TY ++      ++ +VVRTLD G DKPL ++ +  E NP 
Sbjct: 291 RTEFSYLGRHDAPSVEEQAQTYASVLGHFAGQK-VVVRTLDSGSDKPLPFLDLGVEENPA 349

Query: 617 LGLRGIRLCLERPQLLREQFRAILAS--AGFARLHIMLPMVSLLSELHLARKILEEEALA 674
           LG+RG+R+    P  L  Q  A+ A+  A  A L +M PMV+   E     K   E A +
Sbjct: 350 LGIRGLRVGTVYPDTLISQLDALAAAGNATGADLWVMAPMVATADEA----KDFAELARS 405

Query: 675 LGLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSF 734
            G+    K+G MIEVP+AAL A     H+DF SIGTNDL+QYT A+DR    LA   D +
Sbjct: 406 RGIG---KVGAMIEVPAAALRAKDILEHLDFVSIGTNDLSQYTCAVDRMAGGLAQLLDPW 462

Query: 735 HPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATV 794
            PAVL LIA   +A    GK VGVCG  AS+ L  PVL+GLGV  LS+SVP +  ++A +
Sbjct: 463 QPAVLDLIAMVGQAGADAGKPVGVCGESASDPLLAPVLVGLGVTSLSMSVPALGAVRAQL 522

Query: 795 RELDLADCQIIARQVLGLEEAAEVREAL 822
             LDLA C+ +A    G     E R A+
Sbjct: 523 ASLDLAVCKDMAAAARGARNPIEGRAAV 550


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: 993
Number of extensions: 42
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: 838
Length of database: 557
Length adjustment: 39
Effective length of query: 799
Effective length of database: 518
Effective search space:   413882
Effective search space used:   413882
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