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_RS27535 BWI76_RS27535 PTS transporter subunit IIBC

Query= SwissProt::O34521
         (452 letters)



>FitnessBrowser__Koxy:BWI76_RS27535
          Length = 519

 Score =  210 bits (534), Expect = 1e-58
 Identities = 159/507 (31%), Positives = 239/507 (47%), Gaps = 76/507 (14%)

Query: 1   MLSFLQKLGKSFMLPIAVLPAVGIILALGR-----EDVFNIPFVYQAGTAV-------FD 48
           +L  +QK  ++ +  +  LP +G+ILAL         +    F++Q G  +       F 
Sbjct: 8   ILENMQKFSRAMIGAVLFLPVIGLILALSSVLTNPTLISETSFLHQLGQLLGDTFWPLFG 67

Query: 49  HLPLIFAIGIAIGISKDSNGAAGLSGAISYLMLDAATKT--------IDKTN-------- 92
           +L L+F +GI+ G++KD      L   + ++M   A  +         +K N        
Sbjct: 68  NLGLLFCVGISYGLAKDKKTEVALVSVMCFIMFLGANHSWLEHTHGLAEKINGEYYGTGQ 127

Query: 93  ---------NMAVFGGIIAGLIAGYTYNRFKDTKLPEYLGFFSGRRLVPILTAIITIILA 143
                    +M VF GII G    + +N+    +LP  L  + G +L  +    + I  A
Sbjct: 128 TQLLGFVVVDMGVFLGIILGCTIAWVHNKVSTIELPGALSMYGGAKLTLVAMTPVVIFYA 187

Query: 144 GIFGVVWPPIQSCINSFGEWMLGLGGIGAGIFGLFNRLLIPLGLHHVLNNIFW--FQFGE 201
             F   WP +   I +   +M   G  G  ++G F + LIP GLHH +    W  FQ  +
Sbjct: 188 IAFTWFWPFMTHGIAALTGFMKNAGVAGVFVYGFFEKFLIPTGLHHFV----WSPFQLTQ 243

Query: 202 YNG--------VTGDLARFFA--KDPTAGTYMTGFFPIM------MFGLPAACLAMVVTA 245
             G        V+G  A F A  + P     M             +FGL  A LA   TA
Sbjct: 244 IGGTLSVDGQVVSGTQAIFLAYMRHPDLTPVMNEALRFSQQGMTTIFGLAGASLAFYHTA 303

Query: 246 KPSKRKATAGMMIGFALTAFITGITEPIEFAFMFLSPLLYAVHAVLTGLSLFIVNWLGIR 305
           KP K+     +++   +T+ +TGITEPIEF F+F+SPLL+ +HA LT  S  I +   +R
Sbjct: 304 KPEKKMMAKAILLPAIITSMLTGITEPIEFTFLFVSPLLWVIHATLTAASQAICDIFTVR 363

Query: 306 SGFSFSAGAIDYVLSYGIAEKPLL-----LLLVGICYAAVYFIVFYVLIKALNLKTPGRE 360
               + A  +   L Y +     L      +L+GI   AVY+++F  L+  LNLKTPGRE
Sbjct: 364 ---PWGASGLIEFLIYNLPLPVSLTRWPGYVLIGIGQFAVYYVIFRTLVVKLNLKTPGRE 420

Query: 361 DDD-------VDEVLDENTVQDVNENIMLKGLGGKENLQTIDHCATRLRLTVKDTALVDE 413
           DD+        D        Q V  N ++ GLGGKEN+ ++D+C TRLR+ + +  LVD+
Sbjct: 421 DDENVKLYSKADYRKKMGEPQSVT-NEIINGLGGKENIISVDNCFTRLRVAIHNMDLVDD 479

Query: 414 ALLKKAGAKGVVKSGGQSVQVIIGPNV 440
            +LK  GA GVV++  + VQVI G  V
Sbjct: 480 TILKSTGANGVVRNRNE-VQVIYGVKV 505


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: 561
Number of extensions: 29
Number of successful extensions: 6
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: 519
Length adjustment: 34
Effective length of query: 418
Effective length of database: 485
Effective search space:   202730
Effective search space used:   202730
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