GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagEcba in Shewanella sp. ANA-3

Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate 7025672 Shewana3_2822 PTS system, glucose-like IIB subunint (RefSeq)

Query= BRENDA::P09323
         (648 letters)



>FitnessBrowser__ANA3:7025672
          Length = 452

 Score =  259 bits (663), Expect = 1e-73
 Identities = 161/451 (35%), Positives = 247/451 (54%), Gaps = 42/451 (9%)

Query: 33  PDLLNVAFIAQAGGAIFDNLALIFAIGVASSWSKDSAGAAALAGAVGYFVLTKAMVTINP 92
           P++L V  +A  G  IF  + ++FA+ VA  + +D  G AA     GY V+T  +  +  
Sbjct: 19  PEVLTVLMLA-VGKLIFAIMPILFAVAVAIGFCRDQ-GIAAFTAVFGYGVMTATLAALAD 76

Query: 93  --EINMGVLAG---IITGLVGGAAYN-------RWSD-IKLPDFLSFFGGKR-----FVP 134
             ++   +L G   + TG+ GG           RWS  I+LP   SFF G+R      +P
Sbjct: 77  LYQLPTQLLLGMETLDTGIAGGMLIGGVTCFAVRWSQYIRLPAIFSFFEGRRSASLLIIP 136

Query: 135 IATGFFCLVLAAIFGYVWPPVQHAIHAGGEWIV-SAGALGSGIFGFINRLLIPTGLHQVL 193
           +A G     L  I  +VWPP+   I    +W V    A+  G++G + RLLIP GLH + 
Sbjct: 137 LAMG-----LGYILAHVWPPLSLLIERVSDWAVYQKPAIAFGVYGALERLLIPLGLHHIW 191

Query: 194 NTIAWFQIGEFTNAAGTVFHGDINRFYAGDGTAGMFMSGFFPIMMFGLPGAALAMYFAAP 253
           N   + ++G++      V  G++ R+ AGD  AG    G+  I M+GLP AALA++  A 
Sbjct: 192 NAPFYLEVGQYQLQNSEVVRGEVARYLAGDPQAGNLAGGYL-IKMWGLPAAALAIWRCAE 250

Query: 254 KERRPMVGGMLLSVAVTAFLTGVTEPLEFLFMFLAPLLYLLHALLTGISLFVATLLGIHA 313
              R  V G++LS A  ++LTGVTEP+EF FMF+AP L+L+H LL+G++ FV  +L IH 
Sbjct: 251 PSERNRVAGIMLSAAAASWLTGVTEPIEFAFMFVAPFLFLIHVLLSGLAYFVCIMLDIHH 310

Query: 314 GFSFSAGAIDYALMYNLPAASQNVWMLLVMGVIFFAIYFVVFSLVIRMFNLKTPGREDKE 373
              FS G +D+ L+++L   S+N    + +G +   IY+++F   I  FNLKTPGR + +
Sbjct: 311 SIVFSHGLVDFTLLFSL---SRNTGWFVFLGPLTAVIYYLLFRGSILAFNLKTPGRLEPD 367

Query: 374 DEIVTEEANSNTEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTVADSARVNDTMCKR 433
           +             G  +     IAA+GG +N+  ++AC+TRLRL+V     VN     +
Sbjct: 368 E-----------PHGAKESLRAIIAALGGRENIVELNACLTRLRLSVHSPELVNKVRLSQ 416

Query: 434 LGASGVVKLNKQTIQVIVGAKAESIGDAMKK 464
           LGA GV+ + K  +QV+ G KAE++   +++
Sbjct: 417 LGAKGVIVMGK-GVQVVYGTKAETLRKVLQR 446


Lambda     K      H
   0.324    0.139    0.408 

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: 632
Number of extensions: 33
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: 648
Length of database: 452
Length adjustment: 35
Effective length of query: 613
Effective length of database: 417
Effective search space:   255621
Effective search space used:   255621
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 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