Alignments for a candidate for nagEcb in Cronobacter universalis NCTC 9529

GapMind for catabolism of small carbon sources

Alignments for a candidate for nagEcb in Cronobacter universalis NCTC 9529

Align N-Acetyl-D-Glucosamine phosphotransferase system transporter, component of N-acetyl glucosamine-specific PTS permease, GlcNAc IIBC/GlcNAc I-HPr-IIA (characterized)
to candidate WP_167343475.1 AFK65_RS15470 PTS transporter subunit EIIC

Query= TCDB::Q9HXN4
         (570 letters)



>NCBI__GCF_001277175.1:WP_167343475.1
          Length = 518

 Score =  346 bits (887), Expect = 1e-99
 Identities = 206/506 (40%), Positives = 288/506 (56%), Gaps = 55/506 (10%)

Query: 7   ESLQRLGRALMLPIAILPIAGLLLRLGDV----------DLLDI-------PLVHDAGKA 49
           E  QR G++ MLPIA+LP AGLLL +G              LD+        ++  AG  
Sbjct: 15  EKAQRFGKSFMLPIAVLPAAGLLLGVGGALSNPNTLTAYPFLDVGWLQAIFTIMSSAGAI 74

Query: 50  IFANLALIFAIGIAVGFARDNNGTAGLAGAIGYLVMISVLKVI----------DPG---- 95
           +FANL+++FA+G+AVG AR + GTAGLA  + +LVM + +  +          +PG    
Sbjct: 75  VFANLSVLFAVGVAVGLARTDKGTAGLAALLAFLVMNATINALLTLTGQLAQSNPGAVGQ 134

Query: 96  --------IDMGVLSGIISGLVAGALYNRFKDVKLPEYLAFFGGRRFVPIATGISAVCLG 147
                   ++ GV  G++ GLV  AL+ RF  + LP++L FFGG RFVPI + ++A+ +G
Sbjct: 135 GMVLGIQTLETGVFGGVVIGLVTCALHQRFNKIALPQFLGFFGGSRFVPIISALAAIVVG 194

Query: 148 LLFGVIWPPLQQGINGLGQLMLESGSFGAFAFGVLNRLLIVTGLHHILNNLVWFVFGSFT 207
               V+WP  Q+ I GLG L+  +G  G   +G + R+L   GLHHI     W      +
Sbjct: 195 AAMTVVWPHFQKMIFGLGGLVEATGYVGTLLYGFILRMLGPFGLHHIFYLPFWTTALGGS 254

Query: 208 DPETGRVVTGDLARYFA--GDPKGGQF-------MAGMFPVMMFGLPAACLAMYRNARPE 258
           +   G++V G    +FA   DP   QF       M+G F  MMFGL  ACLAMY  A+PE
Sbjct: 255 EIVNGQLVEGTQRIFFAQLADPTTQQFYIGTSRFMSGRFITMMFGLIGACLAMYHTAKPE 314

Query: 259 RRKLIGGLLLSMALTAFLTGVTEPVEFAFMFLAPLLYLLHALLTGLSMALTDLLDIRLGF 318
            +K + GLLLS ALT+FLTG+TEP+EF+F+F+AP+LY++HA   GL+  L  +L I +G 
Sbjct: 315 NKKRVAGLLLSAALTSFLTGITEPIEFSFLFVAPVLYVIHAFFDGLAFMLAHILHITIGQ 374

Query: 319 TFSGGAIDLALG---WGRSTHGWMLWPL-GLLYAGIYYLVFDFCIRRFNLKTPGREDDAS 374
           TFSGG ID  L     G +   W++ PL G+ +  +YY  F F I RF+  TPGRE + +
Sbjct: 375 TFSGGFIDFILFGVLQGEAKTHWLMVPLVGVPWFFLYYFTFRFLITRFDFATPGREKE-T 433

Query: 375 SESGDNAEAERAPAFIRALGGAANLEVVDACTTRLRLRLVDRNKASDAQLKALGAMAVVR 434
            ES    ++ERA A +  LGG  NL+ VD C TRLR+ + D  +  +A LKA GA  V+ 
Sbjct: 434 QESVAMKDSERAQAVVAGLGGRDNLQEVDCCATRLRVTVNDGTQVDEAALKATGARGVIL 493

Query: 435 PGKAGSLQVVVGPQADSIADEIRRAL 460
            G    +QV+ GP    I +EI   L
Sbjct: 494 RG--NGVQVIYGPHVTIIKNEIEELL 517



 Score = 49.3 bits (116), Expect = 4e-10
 Identities = 33/95 (34%), Positives = 49/95 (51%), Gaps = 5/95 (5%)

Query: 474 GSPHTAEEVVAMQATVDAAEAQAWLGALGGAGNLREVRDVALTRLRVSVADERKLATEQL 533
           G     +E VAM+   D+  AQA +  LGG  NL+EV D   TRLRV+V D  ++    L
Sbjct: 428 GREKETQESVAMK---DSERAQAVVAGLGGRDNLQEV-DCCATRLRVTVNDGTQVDEAAL 483

Query: 534 RRLGGQGVSSLAGGICHILVGPRAAALSQALQPLL 568
           +  G +GV     G+  ++ GP    +   ++ LL
Sbjct: 484 KATGARGVILRGNGV-QVIYGPHVTIIKNEIEELL 517


Lambda     K      H
   0.326    0.143    0.428 

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: 723
Number of extensions: 51
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 570
Length of database: 518
Length adjustment: 35
Effective length of query: 535
Effective length of database: 483
Effective search space:   258405
Effective search space used:   258405
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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the 2024 update on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources