GapMind for catabolism of small carbon sources

 

Alignments for a candidate for nagEcba in Cronobacter universalis NCTC 9529

Align protein-Npi-phosphohistidine-N-acetyl-D-glucosamine phosphotransferase (EC 2.7.1.193) (characterized)
to candidate WP_038857764.1 AFK65_RS05470 PTS transporter subunit EIIC

Query= BRENDA::P09323
         (648 letters)



>NCBI__GCF_001277175.1:WP_038857764.1
          Length = 499

 Score =  318 bits (816), Expect = 3e-91
 Identities = 193/494 (39%), Positives = 270/494 (54%), Gaps = 46/494 (9%)

Query: 10  LGRALQLPIAVLPVAALLLRFGQPDLLNVAFIAQAGGAIFDNLALIFAIGVASSWSKDSA 69
           +GRAL LPI++LP A LLL FG  D  ++  +  AGG IFDNL L+FAIG A   + +S 
Sbjct: 17  IGRALMLPISLLPAAGLLLAFG--DKFHLPLMMNAGGVIFDNLPLLFAIGSAVGLASES- 73

Query: 70  GAAALAGAVGYFVLT-------------------KAMVTINPEINMGVLAGIITGLVGGA 110
           G AAL+ AV  F++                     AMV   P + MGV  G+I+G++   
Sbjct: 74  GIAALSAAVSVFIINITISTQLGITPEMAASGGKYAMVVGIPTLQMGVFGGLISGILAAW 133

Query: 111 AYNRWSDIKLPDFLSFFGGKRFVPIATGFFCLVLAAIFGYVWPPVQHAIHAGGEWIVSAG 170
            YNR+  ++LP+FL FF GKRFV IA  F   +L     YVW  +Q  I A    +    
Sbjct: 134 CYNRFHTLQLPEFLGFFSGKRFVAIAAAFLSFLLGLALPYVWQHIQAGIDALSVIVNGDN 193

Query: 171 -ALGSGIFGFINRLLIPTGLHQVLNTIAWFQIGEFTNAAGTVFHGD-----------INR 218
            A  + IFG + R LIP GLH +     W+  G++T   G V HGD           +  
Sbjct: 194 QAASTFIFGLVERALIPLGLHHIWYPSFWYSFGDYTTQTGQVIHGDQTIWFKMLEEGVKS 253

Query: 219 FYAGD-GTAGMFMSGFFPIMMFGLPGAALAMYFAAPKERRPMVGGMLLSVAVTAFLTGVT 277
           F +     AG FM G FP+M+F LP A LAMY  A  + + +  G+L S A+T FLTG+T
Sbjct: 254 FSSNTYQNAGKFMQGEFPLMLFALPAACLAMYHEASTKNKKIASGILFSAALTCFLTGIT 313

Query: 278 EPLEFLFMFLAPLLYLLHALLTGISLFVATLLGIHAGFSFSAGAIDYALMYNLPAAS--- 334
           EP+EF F+F+AP+LY+ +A++ G++     LL  H   SFSAG IDY     LP+ +   
Sbjct: 314 EPVEFTFIFVAPVLYVFNAIMAGLAYMCMYLLDAHIAKSFSAGLIDYISFGILPSFNGYQ 373

Query: 335 QNVWMLLVMGVIFFAIYFVVFSLVIRMFNLKTPGREDKEDEIVTEEANSNTEEGLTQLAT 394
            +    +++G+    IY+  F  VIR F++KTPGR D     VT  A+  T+    +LA 
Sbjct: 374 THYLNAVIVGIPMAIIYYFTFRFVIRRFDVKTPGRVD-----VTASADDKTD---AELAG 425

Query: 395 NYIAAVGGTDNLKAIDACITRLRLTVADSARVNDTMCKRLGASGVVKLNKQTIQVIVGAK 454
           N +  +GG +N+ ++ ACITRLRL VA    V+      LGA GVV +    IQVI GA+
Sbjct: 426 NIVGLLGGKENITSVGACITRLRLEVARPDLVDKDGLNGLGARGVVFVGDNGIQVIFGAR 485

Query: 455 AESIGDAMKKVVAR 468
           A+ I  ++  +  +
Sbjct: 486 AQFIAQSLSGMTGK 499


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: 777
Number of extensions: 40
Number of successful extensions: 7
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: 499
Length adjustment: 36
Effective length of query: 612
Effective length of database: 463
Effective search space:   283356
Effective search space used:   283356
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