GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagPcb in Gracilibacillus halophilus YIM-C55.5

Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate WP_003465872.1 J416_RS04205 PTS transporter subunit EIIC

Query= SwissProt::O34521
         (452 letters)



>NCBI__GCF_000359605.1:WP_003465872.1
          Length = 674

 Score =  353 bits (907), Expect = e-102
 Identities = 203/484 (41%), Positives = 292/484 (60%), Gaps = 54/484 (11%)

Query: 5   LQKLGKSFMLPIAVLPAVGIILALGR-----EDVFNIPF------------VYQAGTAVF 47
           LQK+GK+ MLP+A+LPA GI++A G      + V   P+            + +AG  VF
Sbjct: 8   LQKVGKALMLPVALLPAAGILMAFGTSFAQDQWVEKFPWFGNESVQAVLGVMEEAGGVVF 67

Query: 48  DHLPLIFAIGIAIGISKDSNGAAGLSGAISYLMLDAATKTI-----DKTNNMA------- 95
           D+LPL+FA+G+AIG++K  +G AGL+  I Y++++     I     D T+  A       
Sbjct: 68  DNLPLLFAVGVAIGLAK-GDGVAGLAAIIGYMIMNVTMGEIGGITDDMTSEAAYESMLGV 126

Query: 96  ------VFGGIIAGLIAGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITIILAGIFGVV 149
                 VFGGII G++A Y YNRF + +LP++LGFF+G+R VPI+TA  ++IL  I   V
Sbjct: 127 PTLGTGVFGGIIVGILAAYMYNRFYNIELPQFLGFFAGKRFVPIITAFSSLILGLIMYAV 186

Query: 150 WPPIQSCINSFGEWMLGLGG-IGAGIFGLFNRLLIPLGLHHVLNNIFWFQFGEYNGVTGD 208
           WP  Q  +N+   +ML     +   +FG+  R LIP GLHH+  + FWF+FG Y    G+
Sbjct: 187 WPFAQDGLNAVSHFMLETNRTLSTFVFGIIERALIPFGLHHIFYSPFWFEFGTYTNAAGE 246

Query: 209 LAR-----FFAK-----DPTAGTYMTGFFPIMMFGLPAACLAMVVTAKPSKRKATAGMMI 258
           L R     FF +     D TAG +MTG FP MMFGLPAA LA+  TAKP ++K   G+M 
Sbjct: 247 LIRGDQTIFFEQLKDGVDFTAGNFMTGKFPFMMFGLPAAALAIYHTAKPERKKVVGGIMF 306

Query: 259 GFALTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFIVNWLGIRSGFSFSAGAIDYV 318
             ALT+F+TGITEP+EF+F+F++PLL+A+H V  GLS   +  L ++ G +FS G IDY+
Sbjct: 307 SAALTSFLTGITEPLEFSFLFVAPLLFAIHCVFAGLSFMTMYLLDVKIGMTFSGGFIDYL 366

Query: 319 LSYGIAEKPL---LLLLVGICYAAVYFIVFYVLIKALNLKTPGREDDDVDEVLDENTVQD 375
           L +GI         +++VG+ ++ +Y+  F   I+  NL TPGRE D+ +   DE    D
Sbjct: 367 L-FGIMPNRTDWWWVIIVGLVFSVIYYFGFRFAIQKFNLATPGRE-DEANNAEDEGETDD 424

Query: 376 VNENIMLKGLGGKENLQTIDHCATRLRLTVKDTALVDEALLKKAGAKGVVKSGGQSVQVI 435
               I L  +GG+EN+  +D C TRLR++V D   VD+  LK+ GA GV++  G ++Q I
Sbjct: 425 RPYEI-LTAMGGEENITNLDACITRLRVSVDDKGKVDKDKLKQLGASGVMEV-GNNIQAI 482

Query: 436 IGPN 439
            GP+
Sbjct: 483 YGPS 486


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: 800
Number of extensions: 47
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 452
Length of database: 674
Length adjustment: 36
Effective length of query: 416
Effective length of database: 638
Effective search space:   265408
Effective search space used:   265408
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: 53 (25.0 bits)

This GapMind analysis is from Sep 24 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