GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagPcb in Caulobacter crescentus NA1000

Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate CCNA_00572 CCNA_00572 PTS system, N-acetylglucosamine-specific IIBC component

Query= SwissProt::O34521
         (452 letters)



>FitnessBrowser__Caulo:CCNA_00572
          Length = 582

 Score =  424 bits (1089), Expect = e-123
 Identities = 219/490 (44%), Positives = 313/490 (63%), Gaps = 41/490 (8%)

Query: 2   LSFLQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVYQA---------------GTAV 46
           L  LQ LG++ MLPIAVLP   ++L +G+ D+   P +  A               G A+
Sbjct: 5   LEILQPLGRALMLPIAVLPVAALLLRIGQPDLLGAPALAAATHGMSLSVANTFGAAGGAI 64

Query: 47  FDHLPLIFAIGIAIGISKDSNGAAGLSGAISYLML------------DAATKTIDKTNNM 94
           F  L LIFAIG+A+G++++++GAAGL+G + Y++             + A K ++   ++
Sbjct: 65  FASLGLIFAIGVAVGLARENHGAAGLAGVVCYVIATKGVEALLVAPPEVAAKAVEGAKDL 124

Query: 95  AVFG-------------GIIAGLIAGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITII 141
           A+               GI++G+I+G  YNR+   +LPEYL FF GRR VPI+  +  ++
Sbjct: 125 AIAAWKAKEIGKLSIPVGILSGVISGALYNRYSTIQLPEYLAFFGGRRFVPIVAGLAGVV 184

Query: 142 LAGIFGVVWPPIQSCINSFGEWMLGLGGIGAGIFGLFNRLLIPLGLHHVLNNIFWFQFGE 201
           LA +FG  W  +++ ++     +   G +G  ++GL NRLLI  GLHH+LNN+ WF  G+
Sbjct: 185 LALLFGAFWSTLEAGVDGLSGLVTASGDLGLVVYGLLNRLLIVTGLHHILNNVVWFILGD 244

Query: 202 YNGVTGDLARFFAKDPTAGTYMTGFFPIMMFGLPAACLAMVVTAKPSKRKATAGMMIGFA 261
           +NGVTGDL RF A D TAG +M+GFFP+MMFGLPAACLAM+ TA+P +RKA AGM+   A
Sbjct: 245 FNGVTGDLNRFAAGDKTAGAFMSGFFPVMMFGLPAACLAMLHTARPERRKAVAGMLGSLA 304

Query: 262 LTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYVLSY 321
           LT+F+TG+TEPIEF FMFL+P+L+A+HA+LTGLS+ ++N L ++ GF FSAG  DYVL++
Sbjct: 305 LTSFLTGVTEPIEFTFMFLAPVLFAIHALLTGLSMALMNMLDVKLGFGFSAGLFDYVLNF 364

Query: 322 GIAEKPLLLLLVGICYAAVYFIVFYVLIKALNLKTPGREDDDVDEVLDENTVQDVNENIM 381
             A +PLLL+ VG+ Y A+Y+ VF   I   +LKTPGRED+         T      + M
Sbjct: 365 NKATRPLLLIPVGLVYGALYYGVFRFAILRFDLKTPGREDEAPPSAQAVTTGGGRGAD-M 423

Query: 382 LKGLGGKENLQTIDHCATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNVE 441
           L  LGG  NL ++D C TRLRL V D  LV+E  LK  GA+GVV+   +++QV++GP  +
Sbjct: 424 LAALGGAANLVSVDACTTRLRLIVVDQGLVNEPALKALGARGVVRPSDKALQVVLGPIAD 483

Query: 442 FAAEELRAAV 451
             A E+R A+
Sbjct: 484 TVAGEIRHAI 493



 Score = 52.8 bits (125), Expect = 3e-11
 Identities = 28/68 (41%), Positives = 40/68 (58%)

Query: 381 MLKGLGGKENLQTIDHCATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNV 440
           +L  LGG +NL+ +   A+RLR+ + D   VD+A L  AG +G       +V +IIGP+ 
Sbjct: 514 LLAALGGADNLRDLSVHASRLRVVLNDPERVDQAALHTAGVRGFAAVAPGAVHIIIGPHA 573

Query: 441 EFAAEELR 448
           E  AE LR
Sbjct: 574 ERIAEVLR 581


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: 727
Number of extensions: 33
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: 452
Length of database: 582
Length adjustment: 35
Effective length of query: 417
Effective length of database: 547
Effective search space:   228099
Effective search space used:   228099
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