Alignments for a candidate for treEIIA in Desulfovibrio vulgaris Hildenborough

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Desulfovibrio vulgaris Hildenborough

Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate 206413 DVU0981 multiphosphoryl transfer protein, putative

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



>MicrobesOnline__882:206413
          Length = 854

 Score =  415 bits (1067), Expect = e-120
 Identities = 275/705 (39%), Positives = 373/705 (52%), Gaps = 44/705 (6%)

Query: 152 PSGAVEAVDEEEGDALFSKPLTLPNANGLHARPAAVFAQAAKGFNASIYLHKQTQSANAK 211
           PS A+ A +E          L +PN  GLHARPAA    A   F A + L +  +  +A+
Sbjct: 158 PSSAMPAGEE--------LTLVVPNRLGLHARPAARIVTALGPFAADVQLVRGDRVVSAR 209

Query: 212 SLVAIMALQTVQGDTLQVSAAGEDAEAAIKALVALLAEGCGEAVV--------------- 256
           S+  I  L    G+T+   A G DA  A++A+ AL A   G+A                 
Sbjct: 210 SVNRIATLAVRGGETVTFRAVGGDAALALRAIEALAAAHFGDAPEAPSKGEAPSPAEAPK 269

Query: 257 --NVAEPV--ATQSSATLLRGVCASPGSAFGQVVQVTD----PELVITEQGTGGATERAA 308
             ++AE    A      +LRG  ASPG   G  V        P+  +       ATE   
Sbjct: 270 DGDMAEAAVSADVQGGGVLRGAAASPGLTVGNAVWYRPAFDAPD--VAPLADDPATEVTR 327

Query: 309 LTRGLLAANEALQVLQDK---AAGSAQAEIFRAHQELLEDPTLLEHAH-RLLGEGKSAAF 364
           L   L AA   L  L+ +   AAG  +AEIF  H+ LL+D T+   A  R++   ++A  
Sbjct: 328 LDAALGAARTELVELERRTVAAAGRKEAEIFAMHRLLLDDVTIAGAARQRIMDRREAAES 387

Query: 365 AWNSATLATVTLFQGLGNALIAERAADLADVGQRVLKLILGIQDSAWDLPERAILIAEQL 424
           AW          F+ L    + ER AD+ DVG RVL+L+ G+      L   ++L+A  L
Sbjct: 388 AWYEVISDAAATFRQLPEGYMREREADMVDVGARVLRLLTGVAAVGPRLGGPSVLLATDL 447

Query: 425 TPSQTASLDTRKVLGFVTVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDAD 484
            PS  A+LD   V+G VTV GGATSH AILAR+LG+PA+ G+   +  +  G  V LD  
Sbjct: 448 GPSDMATLDPSLVIGIVTVQGGATSHAAILARSLGIPAVAGLGPALQGVGEGDIVALDGG 507

Query: 485 KGELHLEPNLAEIEQLEAARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEH 544
            G++ + P       +EA R   +   +  +A A+ PA T DG  V + AN+ S  +   
Sbjct: 508 TGDVWVNPAPGVRAAVEARRDAWLAGREAALAGAAAPAVTADGRAVHILANIGSSADAGA 567

Query: 545 ALTLGGEGVGLLRSEFLYLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPL 604
           AL  G EGVGL R+EFL+LDR   P  EEQ   Y   A A+   R +VVRTLD+GGDKP+
Sbjct: 568 ALKNGAEGVGLFRTEFLFLDRTSPPGEEEQLTAYVTAAAAM-QGRPVVVRTLDIGGDKPV 626

Query: 605 AYVP--MDAETNPFLGLRGIRLCLERPQLLREQFRAILASAGFARLHIMLPMVSLLSELH 662
           +Y+      E NPFLGLRGIR CLER  L   Q RA+L +A    L +M PMV+   EL 
Sbjct: 627 SYLEGFATGEDNPFLGLRGIRFCLERKPLFMTQLRALLRAAAVHPLKVMFPMVAHPGELA 686

Query: 663 LARKILEEEALALGLTELP----KLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTL 718
            A+ +L+E    L    +P     +GIMIEVP+A  +AD  A    FFSIGTNDL QY +
Sbjct: 687 AAKALLDEARATLDAEGMPHGQLDVGIMIEVPAAVALADQLARDAAFFSIGTNDLAQYVM 746

Query: 719 AMDRDHPRLANQADSFHPAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVD 778
           A DR +  +A  +D+ HPAVLR++  TV+A HA G  V +CG L     A+P+L+GL +D
Sbjct: 747 AADRGNASVAALSDALHPAVLRMVRDTVRAGHAAGIPVAICGELGGNPEAIPLLVGLELD 806

Query: 779 ELSVSVPLIPTIKATVRELDLADCQIIARQVLGLEEAAEVREALR 823
           ELS++ P IP  K  VR  D   C ++A + + L +AA VR  L+
Sbjct: 807 ELSMNGPAIPRAKEVVRGCDTGTCAVLADRAMALPDAAAVRRLLQ 851


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: 1603
Number of extensions: 84
Number of successful extensions: 8
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: 854
Length adjustment: 42
Effective length of query: 796
Effective length of database: 812
Effective search space:   646352
Effective search space used:   646352
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 17 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)
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 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