Aligments for a candidate for ptsG in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Aligments for a candidate for ptsG in Paraburkholderia bryophila 376MFSha3.1

Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate H281DRAFT_01976 H281DRAFT_01976 PTS system N-acetylglucosamine-specific IIB component, Glc family /PTS system N-acetylglucosamine-specific IIC component, Glc family

Query= BRENDA::P69786
         (477 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_01976 H281DRAFT_01976 PTS
           system N-acetylglucosamine-specific IIB component, Glc
           family /PTS system N-acetylglucosamine-specific IIC
           component, Glc family
          Length = 599

 Score =  383 bits (984), Expect = e-111
 Identities = 213/484 (44%), Positives = 299/484 (61%), Gaps = 38/484 (7%)

Query: 4   NAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVS-HVMAEAGGSVFANMPLI 62
           N F  +Q++G++LMLP++VLP+AG+LL +G       P V +  ++A+AGG++F N+PL+
Sbjct: 4   NPFLKIQRLGRALMLPIAVLPVAGLLLRLGQ------PDVFNIKMIADAGGAIFDNLPLL 57

Query: 63  FAIGVALGFT-NNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEEIASKHLADTGVLGG 121
           FAIGVA+GF  +N+GV+ LA  + Y I V  M            ++I  K   + GVL G
Sbjct: 58  FAIGVAVGFAKDNNGVAGLAGAIGYLIEVAVM------------KDINDK--LNMGVLSG 103

Query: 122 IISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIGSAIQT 181
           I++G +A  ++NR+  IKLP+YL FF GKRFVPI++G+  +  G++  ++W P+ S I T
Sbjct: 104 IVAGIVAGLLYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLALGILFGYVWQPVQSVIDT 163

Query: 182 FSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRYM 241
              W      + AF ++G + R L+  GLHHI N       G +T   G    GD+ R+ 
Sbjct: 164 AGHWLTTAGALGAF-VFGVLNRLLLVTGLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFF 222

Query: 242 AGDPTAGKLSGGFL-FKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPI 300
           AGDPTAG    GF    M+GLPAA +A++H A  E RA VGG++ S ALTSFLTG+TEPI
Sbjct: 223 AGDPTAGTFMTGFFPVMMFGLPAACLAMFHEAPKERRAIVGGLLFSMALTSFLTGVTEPI 282

Query: 301 EFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFPIV 360
           EFSFMF+AP+LY+IHA+L GLA  IC  LG+  G +FS G ID+++  G S+K WL   V
Sbjct: 283 EFSFMFLAPVLYVIHALLTGLALAICSALGIHLGFTFSAGAIDYVLNYGLSTKGWLAIPV 342

Query: 361 GIGYAIVYYTIFRVLIKALDLKTPGREDATEDAK-------------ATGTSEMAPALVA 407
           GI YA+VYY +FR  I+  ++ TPGRE A  D +             A      A   +A
Sbjct: 343 GIVYAVVYYGLFRFFIRKFNMATPGREPAAADEQVDSFAAGGFVSPVAGAAVPRAQRYIA 402

Query: 408 AFGGKENITNLDACITRLRVSVADVSKVDQAGLKKLGAAGVVVAG-SGVQAIFGTKSDNL 466
           A GG  N++ +DAC TRLR+SV D  KV +  LK +GA GV+  G + VQ I G ++D +
Sbjct: 403 ALGGAANLSVVDACTTRLRLSVVDSGKVSENELKTIGARGVLKRGATNVQVIIGPEADII 462

Query: 467 KTEM 470
             E+
Sbjct: 463 ADEI 466



 Score = 35.0 bits (79), Expect = 7e-06
 Identities = 21/44 (47%), Positives = 26/44 (59%), Gaps = 1/44 (2%)

Query: 406 VAAFGGKENITNLDA-CITRLRVSVADVSKVDQAGLKKLGAAGV 448
           +A FGG  N+ +LDA   TRLR+ V D S VD+  L  L  A V
Sbjct: 521 LAVFGGAGNVKSLDAVAATRLRIVVQDPSAVDRQRLATLDTAWV 564


Lambda     K      H
   0.325    0.140    0.422 

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: 896
Number of extensions: 50
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 477
Length of database: 599
Length adjustment: 35
Effective length of query: 442
Effective length of database: 564
Effective search space:   249288
Effective search space used:   249288
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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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