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

GapMind for catabolism of small carbon sources

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

Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (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::P09323
         (648 letters)



>FitnessBrowser__Burk376:H281DRAFT_01976
          Length = 599

 Score =  535 bits (1378), Expect = e-156
 Identities = 268/502 (53%), Positives = 344/502 (68%), Gaps = 13/502 (2%)

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

Query: 68  SAGAAALAGAVGYFVLTKAMVTINPEINMGVLAGIITGLVGGAAYNRWSDIKLPDFLSFF 127
           + G A LAGA+GY +    M  IN ++NMGVL+GI+ G+V G  YNR+ DIKLPD+L+FF
Sbjct: 70  NNGVAGLAGAIGYLIEVAVMKDINDKLNMGVLSGIVAGIVAGLLYNRYKDIKLPDYLAFF 129

Query: 128 GGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGEWIVSAGALGSGIFGFINRLLIPT 187
           GGKRFVPI TG  CL L  +FGYVW PVQ  I   G W+ +AGALG+ +FG +NRLL+ T
Sbjct: 130 GGKRFVPIVTGVVCLALGILFGYVWQPVQSVIDTAGHWLTTAGALGAFVFGVLNRLLLVT 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 MYFAAPKERRPMVGGMLLSVAVTAFLTGVTEPLEFLFMFLAPLLYLLHALLTGISLFVAT 307
           M+  APKERR +VGG+L S+A+T+FLTGVTEP+EF FMFLAP+LY++HALLTG++L + +
Sbjct: 250 MFHEAPKERRAIVGGLLFSMALTSFLTGVTEPIEFSFMFLAPVLYVIHALLTGLALAICS 309

Query: 308 LLGIHAGFSFSAGAIDYALMYNLPAASQNVWMLLVMGVIFFAIYFVVFSLVIRMFNLKTP 367
            LGIH GF+FSAGAIDY L Y L   S   W+ + +G+++  +Y+ +F   IR FN+ TP
Sbjct: 310 ALGIHLGFTFSAGAIDYVLNYGL---STKGWLAIPVGIVYAVVYYGLFRFFIRKFNMATP 366

Query: 368 GRE-----DKEDEIVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTVAD 422
           GRE     ++ D        S         A  YIAA+GG  NL  +DAC TRLRL+V D
Sbjct: 367 GREPAAADEQVDSFAAGGFVSPVAGAAVPRAQRYIAALGGAANLSVVDACTTRLRLSVVD 426

Query: 423 SARVNDTMCKRLGASGVVKLNKQTIQVIVGAKAESIGDAMKKVVAR-----GPVAAASAE 477
           S +V++   K +GA GV+K     +QVI+G +A+ I D ++  + R     G V  A++ 
Sbjct: 427 SGKVSENELKTIGARGVLKRGATNVQVIIGPEADIIADEIRTAMERGGNDAGVVKPAASA 486

Query: 478 ATPATAAPVAKPQAVPNAVSIA 499
           A PA  +  A P A     S A
Sbjct: 487 AAPAAVSTSAAPSATVGGASAA 508



 Score = 35.4 bits (80), Expect = 7e-06
 Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 7/82 (8%)

Query: 396 YIAAVGGTDNLKAIDA-CITRLRLTVADSARVNDTMCKRLGASGVVKLNKQTIQVIVGAK 454
           ++A  GG  N+K++DA   TRLR+ V D + V+    +RL       +   T+ ++VG  
Sbjct: 520 WLAVFGGAGNVKSLDAVAATRLRIVVQDPSAVDR---QRLATLDTAWVAADTVHIVVGDA 576

Query: 455 AESIGDAMKKVVARGPVAAASA 476
           A     A+     R P +  +A
Sbjct: 577 ARRYAQAL---ATRMPASGGAA 595


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: 1105
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: 2
Length of query: 648
Length of database: 599
Length adjustment: 37
Effective length of query: 611
Effective length of database: 562
Effective search space:   343382
Effective search space used:   343382
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.

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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