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

GapMind for catabolism of small carbon sources

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

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate WP_050655247.1 C1M55_RS19650 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::psRCH2:GFF3291
         (960 letters)



>NCBI__GCF_002893965.1:WP_050655247.1
          Length = 557

 Score =  327 bits (837), Expect = 2e-93
 Identities = 226/558 (40%), Positives = 303/558 (54%), Gaps = 21/558 (3%)

Query: 406 DQVNGIAASPGIAIGPVL---VRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLID 462
           +++ GI  S G    P L     +P     P  G SP  EL R+  ALD V  ++ +   
Sbjct: 7   NRIAGIGVSAGSVCAPWLRFSTPEPTSAADPITG-SPEAELIRIREALDAVAEELLSRAK 65

Query: 463 ESQVASIRDIFTTHQAMLKDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDKLL 522
             +  S  +I TT  AM +D  + +  +  L+ GL    A     ++  ++  AL    +
Sbjct: 66  TVEGVSA-EILTTSAAMARDAGIVKAAKANLESGLPTAHAVAVAFDAFCEKLTALGG-YM 123

Query: 523 AERAADLRDVGRRVLACLTG--VEAEQAPDEPYILVMDEVAPSDVATLNAQRVAGILTAG 580
           AERA DLRD+G+R +A L G  +    AP  PYILV  ++AP+D ATL    V G+LTA 
Sbjct: 124 AERATDLRDLGQRAVAVLRGEPMPGIPAPGYPYILVARDLAPADTATLGTSDVVGLLTAE 183

Query: 581 GGATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARSER 640
           GG TSH+AI+A++LGIPA+V    G   LA   LL+LDG  G + + PS    E+A  E 
Sbjct: 184 GGPTSHTAILAKSLGIPAVVNCS-GTDLLAEGKLLILDGTTGTVTIDPSAEMRERAVLEA 242

Query: 641 AAREERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMN 700
           +   E+   A         TRDG  V ++ANIG   +   A A   EG+GL RTE  ++ 
Sbjct: 243 SFVAEQSASAQ----GPGRTRDGFAVRLSANIGTLEDAARAGAADCEGVGLFRTEFSYLG 298

Query: 701 HSQAPNQATQEAEYRRVLEALEGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIRLS 760
              AP+   Q   Y  VL    G+ +VVRTLD G DKPLP+  +  EENP LG+RG+R+ 
Sbjct: 299 RHDAPSVEEQAQTYASVLGHFAGQKVVVRTLDSGSDKPLPFLDLGVEENPALGIRGLRVG 358

Query: 761 LQRPDILETQLRALLAS--ADGRPLRIMFPMVGNIDEWRTAKAMVDRLRVELPVADLQVG 818
              PD L +QL AL A+  A G  L +M PMV   DE   AK   +  R        +VG
Sbjct: 359 TVYPDTLISQLDALAAAGNATGADLWVMAPMVATADE---AKDFAELARSR---GIGKVG 412

Query: 819 IMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRLIGM 878
            MIE+P+AAL A  + + +DF SIGTNDL+QYT A+DR    L+   D   PAVL LI M
Sbjct: 413 AMIEVPAAALRAKDILEHLDFVSIGTNDLSQYTCAVDRMAGGLAQLLDPWQPAVLDLIAM 472

Query: 879 TVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVRELDFAACQR 938
             +A    GK VGVCGE A+D L  P+LVGLGV  LS+S  ++  V+A++  LD A C+ 
Sbjct: 473 VGQAGADAGKPVGVCGESASDPLLAPVLVGLGVTSLSMSVPALGAVRAQLASLDLAVCKD 532

Query: 939 LAQQALMLPGAHEVRAFV 956
           +A  A       E RA V
Sbjct: 533 MAAAARGARNPIEGRAAV 550


Lambda     K      H
   0.317    0.134    0.384 

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: 1141
Number of extensions: 48
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: 960
Length of database: 557
Length adjustment: 40
Effective length of query: 920
Effective length of database: 517
Effective search space:   475640
Effective search space used:   475640
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 24 2021. The underlying query database was built on Sep 17 2021.

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Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources