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

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_050655800.1 C1M55_RS14000 phosphoenolpyruvate--protein phosphotransferase

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



>NCBI__GCF_002893965.1:WP_050655800.1
          Length = 557

 Score =  287 bits (734), Expect = 1e-81
 Identities = 194/563 (34%), Positives = 289/563 (51%), Gaps = 21/563 (3%)

Query: 265 QSSATLLRGVCASPGSAFGQVVQVTD-PELVITEQGTGGATERAALTRGLLAANEALQVL 323
           Q +   + G    PG A+G  +  +  PELV        A   AA    + AA      L
Sbjct: 4   QLNRITVHGTPVVPGIAYGPAIWPSSRPELVTDAPALDEADREAAADAFVAAAKAVENRL 63

Query: 324 QDKAAGS--AQAEIFRAHQELLEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLG 381
             +AA +  A AE+ +A+  +  D   +  A + +  G     A  +AT   V LF  +G
Sbjct: 64  LGRAAEATGAAAEVLQANAAMAADRGWIGAAKKSIAGGVPPVQAAIAATEQFVVLFTKVG 123

Query: 382 NALIAERAADLADVGQRVLKLILGIQDSAWDLPER-AILIAEQLTPSQTASLDTRKVLGF 440
             + AER  DL D+  RV+  + G+ +    +PE  ++L A+ L P+ TA LD  K++G 
Sbjct: 124 GVM-AERVTDLEDIRDRVIAELSGLPEPGVPMPETPSVLCADDLAPADTAGLDATKIIGL 182

Query: 441 VTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQL 500
           VT+ GG TSH AI+AR LG+P I     ++ ++A G  +L+D   G++  EP+  +  +L
Sbjct: 183 VTIFGGPTSHTAIIARQLGIPCIVAAK-ELESIAAGTPILIDGTTGDVIAEPDPEQAREL 241

Query: 501 EAARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEF 560
               + ++ R +  V+  + P  T DG  V+V ANV        A      G+GL R+E 
Sbjct: 242 --VEQSRIDRER--VSTWTGPGRTSDGRPVDVLANVQDGAGARAAALTAAGGIGLFRTEL 297

Query: 561 LYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLR 620
            +L R   P+ +EQA  Y  +  A   ++ +++RTLD G DKPL +     E NP LG+R
Sbjct: 298 CFLGRETEPTVDEQAAIYAEVLEAFAGKK-VIIRTLDAGSDKPLKFANHQEEANPALGVR 356

Query: 621 GIRLCLERPQLLREQFRAILASAGFARLH--IMLPMVSLLSELHLARKILEEEALALGLT 678
           G+R+  +   +L  Q  AI A+A        +M PM++  +E     K   +   A  L 
Sbjct: 357 GVRIAWQDMGILDRQLDAIAAAAASTNSSPWVMAPMIATPAEA----KRFADAVRARDLV 412

Query: 679 ELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFHPAV 738
                G+M+E+P+AAL+AD    HV+F SIGTNDL QYT+A DR    LA+  D + PAV
Sbjct: 413 P----GVMVEIPAAALLADQILEHVEFLSIGTNDLAQYTMAADRMSSELADLTDPWQPAV 468

Query: 739 LRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVRELD 798
           L L+A T +A  A GK VGVCG  A++ L   VL GLGV  LS +   +  + A V  + 
Sbjct: 469 LALVARTAQAGQAAGKRVGVCGEAAADPLLACVLAGLGVSSLSCAAASVAGVGAKVGSVT 528

Query: 799 LADCQIIARQVLGLEEAAEVREA 821
           +A C+  A  VL   +    R+A
Sbjct: 529 MAQCEAAAAAVLATGDPVAARKA 551


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: 948
Number of extensions: 35
Number of successful extensions: 7
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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