Alignments for a candidate for nagPcb in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagPcb in Burkholderia phytofirmans PsJN

Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate BPHYT_RS02745 BPHYT_RS02745 PTS system N-acetylglucosamine-specific transporter subunit IIBC

Query= SwissProt::O34521
         (452 letters)



>FitnessBrowser__BFirm:BPHYT_RS02745
          Length = 591

 Score =  479 bits (1233), Expect = e-139
 Identities = 236/462 (51%), Positives = 318/462 (68%), Gaps = 15/462 (3%)

Query: 5   LQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVYQAGTAVFDHLPLIFAIGIAIGISK 64
           +Q+LG++ MLPIAVLP  G++L LG+ DVFNI  +  AG A+FD+LPL+FAIG+A+G +K
Sbjct: 9   IQRLGRALMLPIAVLPVAGLLLRLGQPDVFNIKMIADAGGAIFDNLPLLFAIGVAVGFAK 68

Query: 65  DSNGAAGLSGAISYLMLDAATKTIDKTNNMAVFGGIIAGLIAGYTYNRFKDTKLPEYLGF 124
           D+NG AGL+GAI YL+  A  K I+   NM V  GI+AG++AG  YNR+KD KLP+YL F
Sbjct: 69  DNNGVAGLAGAIGYLIEVAVMKDINDKLNMGVLSGIVAGIVAGLLYNRYKDIKLPDYLAF 128

Query: 125 FSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGEWMLGLGGIGAGIFGLFNRLLIP 184
           F G+R VPI+T ++ ++L   FG VW P+Q+ I++ G W+   G +GA +FG+ NRLL+ 
Sbjct: 129 FGGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDTAGHWLTTAGALGAFVFGVLNRLLLV 188

Query: 185 LGLHHVLNNIFWFQFGEYN-----GVTGDLARFFAKDPTAGTYMTGFFPIMMFGLPAACL 239
            GLHH+LN++ WF FG +       VTGDL RFFA DPTAGT+MTGFFP+MMFGLPAACL
Sbjct: 189 TGLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFFAGDPTAGTFMTGFFPVMMFGLPAACL 248

Query: 240 AMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFIV 299
           AM   A   +R    G++   ALT+F+TG+TEPIEF+FMFL+P+LY +HA+LTG+SL I 
Sbjct: 249 AMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPIEFSFMFLAPVLYVIHALLTGISLAIC 308

Query: 300 NWLGIRSGFSFSAGAIDYVLSYGIAEKPLLLLLVGICYAAVYFIVFYVLIKALNLKTPGR 359
           + LGI  GF+FSAGAIDYVL+YG++ +    + +G+ Y  VY+ +F   I+  N+ TPGR
Sbjct: 309 SALGIHLGFTFSAGAIDYVLNYGLSTRGWWAIPIGLVYMVVYYGLFRFFIRKFNMATPGR 368

Query: 360 E----DDDVDEVLDENTVQDVNENIM------LKGLGGKENLQTIDHCATRLRLTVKDTA 409
           E    D+ VD       V  V    +      +  LGG  NL  +D C TRLRL+V D+ 
Sbjct: 369 EPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIAALGGASNLSVVDACTTRLRLSVVDSN 428

Query: 410 LVDEALLKKAGAKGVVKSGGQSVQVIIGPNVEFAAEELRAAV 451
            V E  LK  GA+GV+K G  +VQVIIGP  +  A+E+R  +
Sbjct: 429 KVSENELKTIGARGVLKRGSTNVQVIIGPEADIIADEIRTVI 470



 Score = 28.1 bits (61), Expect = 8e-04
 Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 4/63 (6%)

Query: 386 GGKENLQTIDH-CATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNVEFAA 444
           GG  N+ ++D   ATRLR+ V+D + VD   L       +      +  +++G   +  A
Sbjct: 517 GGAGNVLSLDAIAATRLRIVVRDPSAVDRQRLATLDTAWI---SADTFHIVVGDAAQRYA 573

Query: 445 EEL 447
           E+L
Sbjct: 574 EKL 576


Lambda     K      H
   0.326    0.144    0.429 

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: 784
Number of extensions: 44
Number of successful extensions: 4
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: 452
Length of database: 591
Length adjustment: 35
Effective length of query: 417
Effective length of database: 556
Effective search space:   231852
Effective search space used:   231852
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 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