Alignments for a candidate for treEIIA in Desulfobulbus mediterraneus DSM 13871

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Desulfobulbus mediterraneus DSM 13871

Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate WP_028584381.1 G494_RS0109690 phosphoenolpyruvate--protein phosphotransferase

Query= reanno::pseudo3_N2E3:AO353_15995
         (844 letters)



>NCBI__GCF_000429965.1:WP_028584381.1
          Length = 846

 Score =  707 bits (1825), Expect = 0.0
 Identities = 388/836 (46%), Positives = 538/836 (64%), Gaps = 16/836 (1%)

Query: 5   QPLQLLAPLSGVLMPLDHVPDPVFASRVIGDGLCIDPTSQVLCAPLAGVVSNLQHSGHAI 64
           Q + + APLSGV+ PL+ VPDPVF+ +++GDG+ IDP S  L AP  GV+S L  + HA+
Sbjct: 2   QKVLVKAPLSGVIYPLEQVPDPVFSQKLVGDGISIDPVSDQLKAPFPGVISQLHRALHAV 61

Query: 65  SITDDSGVQVLLHIGLDTVNLKGQGFSALVEQGQRVEAGQPLIEFDADYVALHARSLLTL 124
           ++T DSG++V++HIG+DTV LK +GF ALV +GQRVE G+ LI F++D+VA +A+SLLT 
Sbjct: 62  TLTHDSGLEVMIHIGIDTVTLKSKGFKALVREGQRVEQGEVLITFESDFVATNAKSLLTQ 121

Query: 125 MLVVSGEPFSLLTPDSGLVACAQP-VLRLSLGDPRTVVAQEEGEALFSKPVHLPNPNGLH 183
           +++ +GE    +   +G     Q  +L L+L +      +  G  L S+ V +PN  GLH
Sbjct: 122 IILTNGEIVEGVVRAAGFAVEEQTDLLTLTLAEGAAAAVEPSGRQLISEAVIIPNTTGLH 181

Query: 184 ARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTVHGDALQVSAVGEDAELAIS 243
           ARPAAV A  AK F A I L K +  ANAKS+V+IM L   H D +Q+ AVG DA  A+ 
Sbjct: 182 ARPAAVLAGLAKKFQAEIGLLKGEQRANAKSVVSIMKLNVAHLDKVQICAVGPDAAAALE 241

Query: 244 TLAQLLADGCGE-AVTPVAVVAPVVEAQEV---------STKLLRGVCASAGSAFGYVVQ 293
            +   L  G G+   TPV   A +   ++             LL GV A+ G A G   Q
Sbjct: 242 EILPKLESGLGDQGTTPVNSPASLETTEDRYQPPQPKSGDPSLLLGVVAAPGLAVGKAFQ 301

Query: 294 VAERTLEMPEFAADQQLERESLERALMHAT---QALQRLRDNAAGEAQADIFKAHQELLE 350
           + E   +  E A D   E   L+ A+  A    +ALQ      A  A+A IF AH+E+L+
Sbjct: 302 IREERFDFAEEAEDSHRENVRLDAAIETAKNQLEALQAALHKQADPAKAAIFAAHREILD 361

Query: 351 DPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKLIL 410
           DP L+E A++L A+GKS+ +AW     ++A     L + +LA RA DL DVG+RVL+++ 
Sbjct: 362 DPDLIEMARSLTAKGKSSEYAWQRGYTSSAEELSGLSNEILAGRANDLKDVGKRVLRILT 421

Query: 411 GVPDGVWELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPAVC 470
           G       +P+ AILIAE+LTPS TA +DT +V GF T  GGATSHVAILAR+L + AV 
Sbjct: 422 GRESEEHTVPEDAILIAEELTPSFTATIDTDRVRGFCTTTGGATSHVAILARSLNIAAVA 481

Query: 471 GLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAARAAVT 530
           G+    L +A  T ++LDA KG+LH++P    I +  +++   + +H+ +L +A   AV+
Sbjct: 482 GIEAAALEIADATPLILDAGKGQLHINPGDERIARTLSEQAALKAQHELDLAHAHEPAVS 541

Query: 531 RDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIARA 590
            DG   EV AN+  + +  +++ +G EG+GLLRSEFL+ +R  AP+ +EQ   Y  +  A
Sbjct: 542 TDGKAIEVVANIGGVGDALESVQMGGEGVGLLRSEFLFLERLTAPTEEEQYAVYRDVLLA 601

Query: 591 LGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAILSSAG 650
           L   R L+VRTLDVGGDKPL Y+P+  E NPFLG RGIR+ LERP+L R Q RAIL +  
Sbjct: 602 L-EGRPLIVRTLDVGGDKPLPYLPLPREENPFLGQRGIRIGLERPELFRVQARAILRAGA 660

Query: 651 LARLHIMLPMVSQLSELRLARLMLEEEALALGLRELPKLGIMIEVPAAALMADLFAPEVD 710
             ++ IM PM++ + ELR AR MLE+E   LG  E  + GIM+EVPA A+MA+ FA EVD
Sbjct: 661 HGKIRIMFPMIATIQELRDARAMLEQERQKLG-AEPVETGIMVEVPATAVMAEQFAQEVD 719

Query: 711 FFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVCGALAS 770
           FFS+GTNDL+QYTLAMDR HP+LA++ D  +P+VL LI      AH+ GKW+GVCG +A+
Sbjct: 720 FFSVGTNDLSQYTLAMDRGHPKLAAKIDGLNPAVLHLIQLAASGAHSRGKWLGVCGGMAA 779

Query: 771 ETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGLESAEQVRE 826
           +  AVP+LLGLGVDELSV+VP +P+ KA +R+  LS C+++A Q L   S ++VRE
Sbjct: 780 DPQAVPVLLGLGVDELSVAVPALPSTKAVVRQWSLSACKSLARQALACCSGDEVRE 835


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: 1548
Number of extensions: 68
Number of successful extensions: 5
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: 846
Length adjustment: 42
Effective length of query: 802
Effective length of database: 804
Effective search space:   644808
Effective search space used:   644808
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: 56 (26.2 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 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