GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagEcba in Burkholderia phytofirmans PsJN

Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate BPHYT_RS02745 BPHYT_RS02745 PTS system N-acetylglucosamine-specific transporter subunit IIBC

Query= BRENDA::P45604
         (651 letters)



>FitnessBrowser__BFirm:BPHYT_RS02745
          Length = 591

 Score =  545 bits (1405), Expect = e-159
 Identities = 282/493 (57%), Positives = 351/493 (71%), Gaps = 17/493 (3%)

Query: 8   QRLGRALQLPIAVLPVAALLLRFGQPDLLNVPFIAQAGGAIFDNLALIFAIGVASSWSKD 67
           QRLGRAL LPIAVLPVA LLLR GQPD+ N+  IA AGGAIFDNL L+FAIGVA  ++KD
Sbjct: 10  QRLGRALMLPIAVLPVAGLLLRLGQPDVFNIKMIADAGGAIFDNLPLLFAIGVAVGFAKD 69

Query: 68  NAGSAALAGAVGYFVMTKAMVTINPEINMGVLAGIITGLVAGAVYNRWAGIKLPDFLSFF 127
           N G A LAGA+GY +    M  IN ++NMGVL+GI+ G+VAG +YNR+  IKLPD+L+FF
Sbjct: 70  NNGVAGLAGAIGYLIEVAVMKDINDKLNMGVLSGIVAGIVAGLLYNRYKDIKLPDYLAFF 129

Query: 128 GGKRFVPIATGFFCLILAAIFGYVWPPVQHAIHSGGEWIVSAGALGSGIFGFINRLLIPT 187
           GGKRFVPI TG  CL+L   FGYVW PVQ  I + G W+ +AGALG+ +FG +NRLL+ T
Sbjct: 130 GGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDTAGHWLTTAGALGAFVFGVLNRLLLVT 189

Query: 188 GLHQVLNTIAWFQIGEFTNAAGTVFHGDINRFYAGDGTAGMFMSGFFPIMMFGLPGAALA 247
           GLH +LN++ WF  G FT   G    GD++RF+AGD TAG FM+GFFP+MMFGLP A LA
Sbjct: 190 GLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFFAGDPTAGTFMTGFFPVMMFGLPAACLA 249

Query: 248 MYLAAPKARRPMVGGMLLSVAITAFLTGVTEPLEFLFLFLAPLLYLLHAVLTGISLFIAT 307
           M+  APK RR +VGG+L S+A+T+FLTGVTEP+EF F+FLAP+LY++HA+LTGISL I +
Sbjct: 250 MFHEAPKERRAVVGGLLFSMALTSFLTGVTEPIEFSFMFLAPVLYVIHALLTGISLAICS 309

Query: 308 ALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLLVMGVVFFFVYFLLFSAVIRMFNLKTP 367
           ALGIH GF+FSAGAIDYVL Y L   S   W  + +G+V+  VY+ LF   IR FN+ TP
Sbjct: 310 ALGIHLGFTFSAGAIDYVLNYGL---STRGWWAIPIGLVYMVVYYGLFRFFIRKFNMATP 366

Query: 368 GREDKAADVVTEEANSNTEEGLTQ--------LATSYIAAVGGTDNLKAIDACITRLRLT 419
           GRE  AAD   E+ +S    G            A  YIAA+GG  NL  +DAC TRLRL+
Sbjct: 367 GREPAAAD---EQVDSFAAGGFVSPVAGTAVPRAQRYIAALGGASNLSVVDACTTRLRLS 423

Query: 420 VGDSAKVNDAACKRLGASGVVKLNKQTIQVIVGAKAESIGDEMKKVVTRG---PVAAAAA 476
           V DS KV++   K +GA GV+K     +QVI+G +A+ I DE++ V+ +G    V  AAA
Sbjct: 424 VVDSNKVSENELKTIGARGVLKRGSTNVQVIIGPEADIIADEIRTVIAQGGGDAVKPAAA 483

Query: 477 APAGNVATAAPAA 489
           APA  VA A  AA
Sbjct: 484 APAQVVAAAPVAA 496


Lambda     K      H
   0.323    0.138    0.406 

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: 1012
Number of extensions: 63
Number of successful extensions: 5
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 651
Length of database: 591
Length adjustment: 37
Effective length of query: 614
Effective length of database: 554
Effective search space:   340156
Effective search space used:   340156
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 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:

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:

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:

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:

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