GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagEcba in Psychromonas ossibalaenae JAMM 0738

Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate WP_019616713.1 G327_RS0120665 PTS transporter subunit EIIC

Query= BRENDA::P09323
         (648 letters)



>NCBI__GCF_000381745.1:WP_019616713.1
          Length = 485

 Score =  394 bits (1012), Expect = e-114
 Identities = 217/501 (43%), Positives = 302/501 (60%), Gaps = 53/501 (10%)

Query: 1   MNILGFFQRLGRALQLPIAVLPVAALLLRFGQ--------PDLLNVAFIAQAGGAIFDNL 52
           MNILG+FQ++GRAL +P+AVLP AA+L+  G          +    AF+ +AG A+ DN+
Sbjct: 1   MNILGYFQKVGRALMVPVAVLPAAAILMGIGYWIDPNGWGGESQLAAFLIKAGAAVIDNM 60

Query: 53  ALIFAIGVASSWSKDSAGAAALAGAVGYFVLTKAMVTINPEINMGV-------------- 98
           +++FA+GVA   SKD  GAAAL+G VG+ V+T     ++P    G+              
Sbjct: 61  SILFAVGVAYGMSKDKDGAAALSGLVGFLVVT---TLLSPGAVAGIQGIPASEVPFAFNK 117

Query: 99  ----LAGIITGLVGGAAYNRWSDIKLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPP 154
                 GI+ G++    YNR+S ++L   L+FF G+R VPI      ++++ I   VWP 
Sbjct: 118 INNQFVGILVGIISAELYNRFSSVELHKALAFFSGRRLVPIVVSVVMILVSFILMAVWPM 177

Query: 155 VQHAIHAGGEWIVSAGALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHG 214
           +   +   GE I   G +G+G++ F NRLLIP GLH  LN++ WF +             
Sbjct: 178 IFGGLQHFGETISGLGEVGAGLYAFFNRLLIPVGLHHALNSVFWFDVAGIN--------- 228

Query: 215 DINRFYAGD----------GTAGMFMSGFFPIMMFGLPGAALAMYFAAPKERRPMVGGML 264
           DI  F +G           G  GM+ +GFFPIMMFGLPGAA A+Y AA  E +  V  ++
Sbjct: 229 DIPNFLSGQTGIDAGTAIIGKTGMYQAGFFPIMMFGLPGAAFAIYTAAKPENKEKVASIM 288

Query: 265 LSVAVTAFLTGVTEPLEFLFMFLAPLLYLLHALLTGISLFVATLLGIHAGFSFSAGAIDY 324
           L+ A+ +F TGVTEPLEF FMF AP+LY++HA+L+G+S+F A  +   AGF FSAG +D 
Sbjct: 289 LAAALASFFTGVTEPLEFSFMFAAPVLYVIHAVLSGVSVFFAASMEWMAGFGFSAGLVDL 348

Query: 325 ALMYNLPAASQNVWMLLVMGVIFFAIYFVVFSLVIRMFNLKTPGREDKEDEIVTEEANSN 384
            L    P A++  +ML+V G+ FFAIY+  F  VI+  +LKTPGRED E+        + 
Sbjct: 349 VLSSQNPLATK-WYMLIVQGIAFFAIYYFTFLAVIKGLDLKTPGREDAEE----NAPKTK 403

Query: 385 TEEGLTQLATNYIAAVGGTDNLKAIDACITRLRLTVADSARVNDTMCKRLGASGVVKLNK 444
           T E   +LAT Y+AA+GG +NL+ IDACITRLRLT+ D +  N+   K LGA GVVKL +
Sbjct: 404 TTEDAGELATQYVAALGGINNLEVIDACITRLRLTLKDRSEANEAELKALGAMGVVKLGE 463

Query: 445 QTIQVIVGAKAESIGDAMKKV 465
             +QVI+G +AESI + MK V
Sbjct: 464 NNLQVIIGPQAESIANRMKAV 484


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: 820
Number of extensions: 39
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: 648
Length of database: 485
Length adjustment: 36
Effective length of query: 612
Effective length of database: 449
Effective search space:   274788
Effective search space used:   274788
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: 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