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

GapMind for catabolism of small carbon sources

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

Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate H281DRAFT_01853 H281DRAFT_01853 PTS system D-glucose-specific IIB component, Glc family /PTS system D-glucose-specific IIC component, Glc family

Query= BRENDA::P09323
         (648 letters)



>FitnessBrowser__Burk376:H281DRAFT_01853
          Length = 596

 Score =  367 bits (942), Expect = e-106
 Identities = 218/516 (42%), Positives = 305/516 (59%), Gaps = 38/516 (7%)

Query: 5   GFFQRLGRALQLPIAVLPVAALLLRFGQPDL------LNVAFIAQAGGAIFDNLALIFAI 58
           G  Q++G++L LP+AVLPVA LLL  G  D       + +A +  AG  IF NL LIFAI
Sbjct: 7   GVLQKVGKSLMLPVAVLPVAGLLLGLGATDFHGYVPAIVLALMKNAGDVIFANLPLIFAI 66

Query: 59  GVASSWSKDSAGAAALAGAVGYFVLTKAMVTIN-------------PEINMGVLAGIITG 105
           GVA  ++++  G + +A  +GY V+T  +  I              P I  GV  GI+ G
Sbjct: 67  GVALGFTEND-GVSGIAATIGYLVMTATLGVIAKVEGIEPDMIMGIPSIQTGVFGGILAG 125

Query: 106 LVGGAAYNRWSDIKLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGEW 165
            +    +NR+  I LP +L FF GKRFVPI T    +VL AI   VWPP+  AI A  +W
Sbjct: 126 GLAAWMFNRYYRIALPAYLGFFAGKRFVPIVTAIGSIVLGAILSVVWPPIGSAIKAFSQW 185

Query: 166 I-VSAGALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTN-AAGTVFHGDINRFYAGD 223
             VS     + ++GF+ RLLIP GLH + N   +F+ G F +   G V HGDI RF+AGD
Sbjct: 186 AAVSDPRTAATVYGFVERLLIPFGLHHIWNVPFFFEAGSFLDPTTGKVVHGDITRFFAGD 245

Query: 224 GTAGMFMSGFFPIMMFGLPGAALAMYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFL 283
            TAG+ ++G F   MFGLP AA+A++  A  E +  VGGM++S A+T+FLTG+TEP+EF 
Sbjct: 246 RTAGI-LAGAFLFKMFGLPAAAIAIWHCAKPENKVAVGGMMVSAALTSFLTGITEPIEFA 304

Query: 284 FMFLAPLLYLLHALLTGISLFVATLLGIHAGFSFSAGAIDYALMYNLPA-ASQNVWMLLV 342
           F+F+AP+LYL+HA L   + FVA  LG+  GF+FS G ID+ LM+NL    S + W + +
Sbjct: 305 FLFVAPVLYLIHACLAASAQFVANTLGMRMGFTFSQGGIDF-LMFNLIGNKSTHAWYVFI 363

Query: 343 MGVIFFAIYFVVFSLVIRMFNLKTPGREDKEDEIVTEEANSNTEEGLTQLATNYIAAVGG 402
           +G I+  IY+ VF  VI  F+LKTPGRED      T E    +  G+   +   + A GG
Sbjct: 364 LGPIYAVIYYGVFRFVITRFDLKTPGREDD-----TVETAKVSTAGVGGRSRELVLAFGG 418

Query: 403 TDNLKAIDACITRLRLTVADSARVNDTMCKRLGASGVVKLNKQTIQVIVGAKAES----I 458
             N+ ++DACITRLR++V + A VN+   K LGA+GVV++    +Q I G  +E+    +
Sbjct: 419 RSNIDSLDACITRLRISVKNPALVNEGKLKALGAAGVVRVG-NGVQAIFGPLSENMKTDM 477

Query: 459 GDAMKKVVARGPVAA---ASAEATPATAAPVAKPQA 491
            + +K   +   +AA   A AEA  +TA  +   QA
Sbjct: 478 HEYLKTAGSEADLAADGKAVAEAAASTATAIGSAQA 513



 Score = 38.1 bits (87), Expect = 1e-06
 Identities = 21/67 (31%), Positives = 36/67 (53%), Gaps = 1/67 (1%)

Query: 398 AAVGGTDNLKAIDA-CITRLRLTVADSARVNDTMCKRLGASGVVKLNKQTIQVIVGAKAE 456
           AA+GG  N++ +DA   TRLR+ + D+++++    K  G      L      +IVG  A 
Sbjct: 530 AALGGVANIQKLDALAATRLRVGLRDASQLDTAALKAAGVPATQTLTNGEFDLIVGLDAP 589

Query: 457 SIGDAMK 463
           ++  AM+
Sbjct: 590 NLAGAMR 596


Lambda     K      H
   0.324    0.139    0.408 

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: 939
Number of extensions: 41
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: 648
Length of database: 596
Length adjustment: 37
Effective length of query: 611
Effective length of database: 559
Effective search space:   341549
Effective search space used:   341549
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: 41 (22.0 bits)
S2: 54 (25.4 bits)

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

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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