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:

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