Alignments for a candidate for treEIIA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Paraburkholderia bryophila 376MFSha3.1

Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate H281DRAFT_01852 H281DRAFT_01852 Phosphocarrier protein HPr/phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9)/PTS system IIA component, Glc family (TC 4.A.1)

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



>FitnessBrowser__Burk376:H281DRAFT_01852
          Length = 851

 Score =  760 bits (1963), Expect = 0.0
 Identities = 421/842 (50%), Positives = 557/842 (66%), Gaps = 23/842 (2%)

Query: 7   LQLLAPLSGVLMPLDHVPDPVFASRVIGDGLCIDPTSQVLCAPLAGVVSNLQHSGHAISI 66
           ++L+APLSGV++PL+ VPDPVFA +++GDG+ IDPTS  L +PL G V+ L  S HA++I
Sbjct: 10  IELVAPLSGVMVPLETVPDPVFAQKMVGDGISIDPTSHELLSPLPGKVTQLHSSSHAVTI 69

Query: 67  TDDSGVQVLLHIGLDTVNLKGQGFSALVEQGQRVEAGQPLIEFDADYVALHARSLLTLML 126
           T  SG++VLLHIGLDTV L+G+GF+ LV++G  V  GQPLI FD  YV   A SLLT M+
Sbjct: 70  TGASGLEVLLHIGLDTVLLRGEGFTPLVKEGDTVATGQPLIRFDPVYVGAKAASLLTQMV 129

Query: 127 VVSGEPFSLLTPDSGLVACAQPV-LRLSLGDP--RTVVAQEEGEALFSKPVHLPNPNGLH 183
           + +G+  +   P  GLV  A  V L + L D   +   A+  G A+ S  V LPNP G+H
Sbjct: 130 IANGDRVTRYVPAEGLVTAAGDVALTVELADDTAKDQTARTTG-AIVSDEVTLPNPAGMH 188

Query: 184 ARPAAVFAQAAKGFAASICLHKQQDSANAKSLVAIMALQTVHGDALQVSAVGEDAELAIS 243
           ARPAAVF  AAK + + I L    +SANAKS+V+IM L T  GD +++ A G DA  A S
Sbjct: 189 ARPAAVFVGAAKKYESEIRLLHGSNSANAKSIVSIMGLATKFGDRVRIQATGPDAGEAAS 248

Query: 244 TLAQLLADGCGE------AVTPVAVV---------APVVEAQEVSTKLLRGVCASAGSAF 288
            LA+LLA+G GE      A  P ++          A V  AQ      L GV AS G A 
Sbjct: 249 VLARLLAEGSGEKPADAPAFPPTSLAPASGSSGEPAVVKRAQPADVNELTGVSASPGLAV 308

Query: 289 GYVVQVAERTLEMPEFAADQQLERESLERALMHATQALQRLRDNAAGEAQADIFKAHQEL 348
           G +VQ  ++ +++ E     Q ER  LE A   A Q ++ L+      ++A I  AH EL
Sbjct: 309 GKIVQFRQQVIDVKEAGESPQRERVRLEAAHHEARQNIEALKAKLTDPSKAQILDAHLEL 368

Query: 349 LEDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQRVLKL 408
           LEDP L   A   I+EGKSA FAW +A E  A   + L + LL ERA D+ DVG+RVL L
Sbjct: 369 LEDPDLNGMAIGSISEGKSAGFAWRAAFEQQAATLEKLDNPLLRERAGDVRDVGRRVLAL 428

Query: 409 ILGVPDGVWELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARALGLPA 468
           + G+     ++P  +ILIAE+L+PS TA+LD  KVLGF T  GGATSHVAILAR+LG+PA
Sbjct: 429 LAGMQQAQIDVPAGSILIAEELSPSDTASLDRTKVLGFCTTTGGATSHVAILARSLGIPA 488

Query: 469 VCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENAARAA 528
           +CG+    L LA GT V+LD   G L  +P+   +E+   +  +Q ++ + E   A++ A
Sbjct: 489 ICGIDEDALQLADGTLVVLDGSHGSLRRNPSAGEVEKARERISRQAEKREEEKLAASKLA 548

Query: 529 VTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTYSAIA 588
           +T DGH  EV AN+ +  E   A++ GAEG+GLLRSEFL+  R  APS DEQA  Y A+A
Sbjct: 549 MTADGHRVEVVANIRNAKEARDAVAAGAEGVGLLRSEFLFDDRDTAPSEDEQASEYCAVA 608

Query: 589 RALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRAILSS 648
            ALG +R LV+RTLD GGDKPL+Y+P+  E NPFLG+RG+R+ L+RP + R Q RAIL +
Sbjct: 609 EALGRERPLVIRTLDAGGDKPLSYMPLPKEDNPFLGLRGVRVSLDRPDIFRTQLRAILRA 668

Query: 649 AGLARLHIMLPMVSQLSELRLARLMLEEEALALGLR-ELPKLGIMIEVPAAALMADLFAP 707
           A +  LH+M PMV+ + E+  A+ +L EEA   G R    K+G+MIEVPAAAL+A+  A 
Sbjct: 669 APIGNLHVMFPMVAAIEEVLAAKKILLEEA---GDRANSIKVGVMIEVPAAALIAEPLAR 725

Query: 708 EVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIASTVKAAHAHGKWVGVCGA 767
           EVDFFSIGTNDLTQYTLAMDR HP+LA QAD+ HP+VLRLI  TV+ AH HGKWVGVCG 
Sbjct: 726 EVDFFSIGTNDLTQYTLAMDRGHPKLARQADALHPAVLRLIGMTVEGAHKHGKWVGVCGG 785

Query: 768 LASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAIAHQVLGLESAEQVREA 827
           +AS+ +AVP+L+GLGVDELSVSVP + +IKA +  + ++  + +A +V+ L +A +VR  
Sbjct: 786 IASDAIAVPVLVGLGVDELSVSVPAVGSIKAQLARLTMAQARQLAAEVVRLGTAAEVRAL 845

Query: 828 LS 829
           L+
Sbjct: 846 LA 847


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: 1575
Number of extensions: 57
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: 844
Length of database: 851
Length adjustment: 42
Effective length of query: 802
Effective length of database: 809
Effective search space:   648818
Effective search space used:   648818
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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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 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