GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ptsG in Cronobacter universalis NCTC 9529

Align protein-Npi-phosphohistidine-D-glucose phosphotransferase (EC 2.7.1.199) (characterized)
to candidate WP_038857764.1 AFK65_RS05470 PTS transporter subunit EIIC

Query= BRENDA::P69786
         (477 letters)



>NCBI__GCF_001277175.1:WP_038857764.1
          Length = 499

 Score =  353 bits (905), Expect = e-101
 Identities = 202/487 (41%), Positives = 284/487 (58%), Gaps = 32/487 (6%)

Query: 2   FKNAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVSHVMAEAGGSVFANMPL 61
           F  + + L  +G++LMLP+S+LP AG+LL  G      LP     +M  AGG +F N+PL
Sbjct: 7   FVKSLSKLSMIGRALMLPISLLPAAGLLLAFGDKFH--LP-----LMMNAGGVIFDNLPL 59

Query: 62  IFAIGVALGFTNNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPAEE-----IASKHLADT 116
           +FAIG A+G  +  G++AL+A V+  I+  T++    +   + A       +        
Sbjct: 60  LFAIGSAVGLASESGIAALSAAVSVFIINITISTQLGITPEMAASGGKYAMVVGIPTLQM 119

Query: 117 GVLGGIISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVVLSFIWPPIG 176
           GV GG+ISG +AA+ +NRF+ ++LPE+LGFF+GKRFV I +   +   G+ L ++W  I 
Sbjct: 120 GVFGGLISGILAAWCYNRFHTLQLPEFLGFFSGKRFVAIAAAFLSFLLGLALPYVWQHIQ 179

Query: 177 SAIQTFSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGD 236
           + I   S      N   +  I+G +ER L+P GLHHIW   F    G+YT   GQV HGD
Sbjct: 180 AGIDALSVIVNGDNQAASTFIFGLVERALIPLGLHHIWYPSFWYSFGDYTTQTGQVIHGD 239

Query: 237 -----------IPRYMAGD-PTAGK-LSGGFLFKMYGLPAAAIAIWHSAKPENRAKVGGI 283
                      +  + +     AGK + G F   ++ LPAA +A++H A  +N+    GI
Sbjct: 240 QTIWFKMLEEGVKSFSSNTYQNAGKFMQGEFPLMLFALPAACLAMYHEASTKNKKIASGI 299

Query: 284 MISAALTSFLTGITEPIEFSFMFVAPILYIIHAILAGLAFPICILLGMRDGTSFSHGLID 343
           + SAALT FLTGITEP+EF+F+FVAP+LY+ +AI+AGLA+    LL      SFS GLID
Sbjct: 300 LFSAALTCFLTGITEPVEFTFIFVAPVLYVFNAIMAGLAYMCMYLLDAHIAKSFSAGLID 359

Query: 344 FI------VLSGNSSKLWLFPIVGIGYAIVYYTIFRVLIKALDLKTPGREDATEDAKATG 397
           +I        +G  +      IVGI  AI+YY  FR +I+  D+KTPGR D T  A    
Sbjct: 360 YISFGILPSFNGYQTHYLNAVIVGIPMAIIYYFTFRFVIRRFDVKTPGRVDVTASADDKT 419

Query: 398 TSEMAPALVAAFGGKENITNLDACITRLRVSVADVSKVDQAGLKKLGAAGVVVAG-SGVQ 456
            +E+A  +V   GGKENIT++ ACITRLR+ VA    VD+ GL  LGA GVV  G +G+Q
Sbjct: 420 DAELAGNIVGLLGGKENITSVGACITRLRLEVARPDLVDKDGLNGLGARGVVFVGDNGIQ 479

Query: 457 AIFGTKS 463
            IFG ++
Sbjct: 480 VIFGARA 486


Lambda     K      H
   0.325    0.140    0.422 

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: 699
Number of extensions: 28
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: 477
Length of database: 499
Length adjustment: 34
Effective length of query: 443
Effective length of database: 465
Effective search space:   205995
Effective search space used:   205995
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: 40 (21.6 bits)
S2: 52 (24.6 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