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

GapMind for catabolism of small carbon sources

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

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (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::psRCH2:GFF3291
         (960 letters)



>FitnessBrowser__Burk376:H281DRAFT_01852
          Length = 851

 Score =  544 bits (1402), Expect = e-159
 Identities = 319/681 (46%), Positives = 423/681 (62%), Gaps = 18/681 (2%)

Query: 284 SAQVPLANAHGLHARPAKVLTEIAQAFEGEIRVRLAGTESAGVSVKSLSKLLAMGAHRGQ 343
           S +V L N  G+HARPA V    A+ +E EIR+ L G+ SA  + KS+  ++ +    G 
Sbjct: 176 SDEVTLPNPAGMHARPAAVFVGAAKKYESEIRL-LHGSNSA--NAKSIVSIMGLATKFGD 232

Query: 344 LLEFMAEPAIASDALPALVRAVEEGLGEEVEPLPAPGEASEPPVTAQGPAESAIDQAALR 403
            +   A    A +A   L R + EG GE+    PA    S  P +      + + +A   
Sbjct: 233 RVRIQATGPDAGEAASVLARLLAEGSGEKPADAPAFPPTSLAPASGSSGEPAVVKRAQPA 292

Query: 404 AGDQVNGIAASPGIAIGPVLVRKPQVIDYPKRGESPVIELQRLDAALDKVHADIGTLIDE 463
             +++ G++ASPG+A+G ++  + QVID  + GESP  E  RL+AA  +   +I  L  +
Sbjct: 293 DVNELTGVSASPGLAVGKIVQFRQQVIDVKEAGESPQRERVRLEAAHHEARQNIEALKAK 352

Query: 464 SQVASIRDIFTTHQAMLKDPALREEVQVRLQKGLSAEAAWMEEIESAAQQQEALHDKLLA 523
               S   I   H  +L+DP L       + +G SA  AW    E  A   E L + LL 
Sbjct: 353 LTDPSKAQILDAHLELLEDPDLNGMAIGSISEGKSAGFAWRAAFEQQAATLEKLDNPLLR 412

Query: 524 ERAADLRDVGRRVLACLTGVEAEQAPDEPY--ILVMDEVAPSDVATLNAQRVAGILTAGG 581
           ERA D+RDVGRRVLA L G++  Q  D P   IL+ +E++PSD A+L+  +V G  T  G
Sbjct: 413 ERAGDVRDVGRRVLALLAGMQQAQI-DVPAGSILIAEELSPSDTASLDRTKVLGFCTTTG 471

Query: 582 GATSHSAIIARALGIPAIVGAGPGVLGLARNTLLLLDGERGELLVAPSGAQLEQARSERA 641
           GATSH AI+AR+LGIPAI G     L LA  TL++LDG  G L   PS  ++E+AR   +
Sbjct: 472 GATSHVAILARSLGIPAICGIDEDALQLADGTLVVLDGSHGSLRRNPSAGEVEKARERIS 531

Query: 642 AREERKHLANERRMDAAVTRDGHPVEIAANIGAAGETPEAVAMGAEGIGLLRTELVFMNH 701
            + E++          A+T DGH VE+ ANI  A E  +AVA GAEG+GLLR+E +F + 
Sbjct: 532 RQAEKREEEKLAASKLAMTADGHRVEVVANIRNAKEARDAVAAGAEGVGLLRSEFLFDDR 591

Query: 702 SQAPNQATQEAEYRRVLEAL-EGRPLVVRTLDVGGDKPLPYWPMPAEENPFLGVRGIRLS 760
             AP++  Q +EY  V EAL   RPLV+RTLD GGDKPL Y P+P E+NPFLG+RG+R+S
Sbjct: 592 DTAPSEDEQASEYCAVAEALGRERPLVIRTLDAGGDKPLSYMPLPKEDNPFLGLRGVRVS 651

Query: 761 LQRPDILETQLRALLASADGRPLRIMFPMVGNIDEWRTAKAMV-----DRLRVELPVADL 815
           L RPDI  TQLRA+L +A    L +MFPMV  I+E   AK ++     DR         +
Sbjct: 652 LDRPDIFRTQLRAILRAAPIGNLHVMFPMVAAIEEVLAAKKILLEEAGDRAN------SI 705

Query: 816 QVGIMIEIPSAALIAPVLAQEVDFFSIGTNDLTQYTLAIDRGHPTLSGQADGLHPAVLRL 875
           +VG+MIE+P+AALIA  LA+EVDFFSIGTNDLTQYTLA+DRGHP L+ QAD LHPAVLRL
Sbjct: 706 KVGVMIEVPAAALIAEPLAREVDFFSIGTNDLTQYTLAMDRGHPKLARQADALHPAVLRL 765

Query: 876 IGMTVEAAHAHGKWVGVCGELAADALAVPLLVGLGVDELSVSARSIALVKARVRELDFAA 935
           IGMTVE AH HGKWVGVCG +A+DA+AVP+LVGLGVDELSVS  ++  +KA++  L  A 
Sbjct: 766 IGMTVEGAHKHGKWVGVCGGIASDAIAVPVLVGLGVDELSVSVPAVGSIKAQLARLTMAQ 825

Query: 936 CQRLAQQALMLPGAHEVRAFV 956
            ++LA + + L  A EVRA +
Sbjct: 826 ARQLAAEVVRLGTAAEVRALL 846


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: 1773
Number of extensions: 73
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: 960
Length of database: 851
Length adjustment: 43
Effective length of query: 917
Effective length of database: 808
Effective search space:   740936
Effective search space used:   740936
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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Protein sequences (fasta format)
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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, or view the source code.

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