GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagPcb in Klebsiella michiganensis M5al

Align PTS system N-acetylglucosamine-specific EIICB component; EIICB-Nag; EC 2.7.1.- (characterized)
to candidate BWI76_RS08220 BWI76_RS08220 PTS N-acetyl glucosamine transporter subunit IIABC

Query= SwissProt::O34521
         (452 letters)



>FitnessBrowser__Koxy:BWI76_RS08220
          Length = 650

 Score =  478 bits (1230), Expect = e-139
 Identities = 237/465 (50%), Positives = 318/465 (68%), Gaps = 15/465 (3%)

Query: 1   MLSFLQKLGKSFMLPIAVLPAVGIILALGREDVFNIPFVYQAGTAVFDHLPLIFAIGIAI 60
           +L F Q+LG++  LPIAVLP   ++L  G+ D+ NI F+ QAG A+FD+L LIFAIG+A 
Sbjct: 3   ILGFFQRLGRALQLPIAVLPVAALLLRFGQPDLLNISFIAQAGGAIFDNLALIFAIGVAS 62

Query: 61  GISKDSNGAAGLSGAISYLMLDAATKTIDKTNNMAVFGGIIAGLIAGYTYNRFKDTKLPE 120
             SKDS GAA L+GA+ Y +L  A  TI+   NM V  GII GL+ G  YNR+   KLP+
Sbjct: 63  SWSKDSAGAAALAGAVGYFVLTKAMVTINPAINMGVLAGIITGLVGGAVYNRWSGIKLPD 122

Query: 121 YLGFFSGRRLVPILTAIITIILAGIFGVVWPPIQSCINSFGEWMLGLGGIGAGIFGLFNR 180
           +L FF G+R VPI T    ++LA IFG VWPP+Q+ I++ GEW++G G +G+GIFG  NR
Sbjct: 123 FLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQNAIHAGGEWIVGAGALGSGIFGFINR 182

Query: 181 LLIPLGLHHVLNNIFWFQFGEYNGVT-----GDLARFFAKDPTAGTYMTGFFPIMMFGLP 235
           LLIP GLH VLN I WFQ GE+         GD+ RF+A D TAG +M+GFFPIMMFGLP
Sbjct: 183 LLIPTGLHQVLNTIAWFQIGEFTNAAGAVFHGDINRFYAGDGTAGMFMSGFFPIMMFGLP 242

Query: 236 AACLAMVVTAKPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLS 295
            A LAM   A   +R    GM++  A+TAF+TG+TEP+EF FMFL+PLLY +HA+LTG+S
Sbjct: 243 GAALAMYFAAPKERRPMVGGMLLSVAITAFLTGVTEPLEFLFMFLAPLLYLLHAILTGIS 302

Query: 296 LFIVNWLGIRSGFSFSAGAIDYVLSYGI---AEKPLLLLLVGICYAAVYFIVFYVLIKAL 352
           LF+   LGI +GFSFSAGAIDYVL Y +   ++   +L+++G+ +  +YF++F  +I+  
Sbjct: 303 LFVATALGIHAGFSFSAGAIDYVLMYSLPAASKNVWMLIVMGVVFFVIYFLLFSAVIRMF 362

Query: 353 NLKTPGREDDDVDEVLDENTVQDVNENI------MLKGLGGKENLQTIDHCATRLRLTVK 406
           NLKTPGRE D VD+V+ E    +  E +       +  +GG +NL+ ID C TRLRLTV 
Sbjct: 363 NLKTPGRE-DKVDDVVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTVA 421

Query: 407 DTALVDEALLKKAGAKGVVKSGGQSVQVIIGPNVEFAAEELRAAV 451
           D+ALV++A  K+ GA GVVK   Q++QVI+G   E   +E++  V
Sbjct: 422 DSALVNDAACKRLGASGVVKLNKQTIQVIVGAKAESVGDEMKKVV 466


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: 756
Number of extensions: 38
Number of successful extensions: 5
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: 650
Length adjustment: 35
Effective length of query: 417
Effective length of database: 615
Effective search space:   256455
Effective search space used:   256455
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