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-acetylglucosamine-specific PTS system, IIBC components (nagE) (characterized)
to candidate WP_015740856.1 AFK65_RS07765 PTS glucose transporter subunit IIBC

Query= reanno::BFirm:BPHYT_RS02745
         (591 letters)



>NCBI__GCF_001277175.1:WP_015740856.1
          Length = 477

 Score =  374 bits (961), Expect = e-108
 Identities = 209/484 (43%), Positives = 297/484 (61%), Gaps = 38/484 (7%)

Query: 4   NPFLKIQRLGRALMLPIAVLPVAGLLLRLGQ------PDVFNIKMIADAGGAIFDNLPLL 57
           N F  +Q++G++LMLP++VLP+AG+LL +G       P V +  ++A+AGG++F N+PL+
Sbjct: 4   NAFANLQKVGKSLMLPVSVLPIAGILLGVGSANFSWLPAVVS-HVMAEAGGSVFANMPLI 62

Query: 58  FAIGVAVGFAKDNNGVAGLAGAIGYLIEVAVM------------KDINDK--LNMGVLSG 103
           FAIGVA+GF  +N+GV+ LA  + Y I V  M            ++I  K   + GVL G
Sbjct: 63  FAIGVALGFT-NNDGVSALAAVVAYGIMVKTMAVVAPLVLHLPPEEIAAKHLADTGVLGG 121

Query: 104 IVAGIVAGLLYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDT 163
           I++G +A  ++NR+  IKLP+YL FF GKRFVPI++G+  +  G+   ++W P+ + I T
Sbjct: 122 IISGAIAAYMFNRFYRIKLPEYLGFFAGKRFVPIISGLAAIFTGVILSFIWPPIGSAIQT 181

Query: 164 AGHWLTTAGALGAF-VFGVLNRLLLVTGLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFF 222
              W      + AF ++G + R L+  GLHHI N       G +T   G    GD+ R+ 
Sbjct: 182 FSQWAAYQNPVVAFGIYGFIERCLVPFGLHHIWNVPFQMQIGEYTNAAGQVFHGDIPRYM 241

Query: 223 AGDPTAGTFMTGFFPVMMFGLPAACLAMFHEAPKERRAVVGGLLFSMALTSFLTGVTEPI 282
           AGDPTAG    GF    M+GLPAA +A++H A  E RA VGG++ S ALTSFLTG+TEPI
Sbjct: 242 AGDPTAGKLSGGFL-FKMYGLPAAAIAIWHSAKPENRAKVGGIMISAALTSFLTGITEPI 300

Query: 283 EFSFMFLAPVLYVIHALLTGISLAICSALGIHLGFTFSAGAIDYVLNYGLSTRGWWAIPI 342
           EFSFMF+AP+LYVIHA+L G++  IC  LG+  G +FS G ID+++  G S++ W    +
Sbjct: 301 EFSFMFVAPILYVIHAILAGLAFPICILLGMRDGTSFSHGLIDFIVLSGNSSKLWLFPIV 360

Query: 343 GLVYMVVYYGLFRFFIRKFNMATPGREPAAADEQVDSFAAGGFVSPVAGTAVPRAQRYIA 402
           G  Y VVYY +FR  I+  ++ TPGRE A  D            +   GT+   A   +A
Sbjct: 361 GACYAVVYYTIFRVLIKALDLKTPGREDATED------------TKATGTS-EMAPALVA 407

Query: 403 ALGGASNLSVVDACTTRLRLSVVDSNKVSENELKTIGARGVLKRGSTNVQVIIGPEADII 462
           A GG  N++ +DAC TRLR+SV D  KV +  LK +GA GV+  GS  VQ I G ++D +
Sbjct: 408 AFGGKENITNLDACITRLRVSVADVAKVDQAGLKKLGAAGVVVAGS-GVQAIFGTKSDNL 466

Query: 463 ADEI 466
             E+
Sbjct: 467 KTEM 470



 Score = 33.9 bits (76), Expect = 2e-05
 Identities = 22/58 (37%), Positives = 30/58 (51%), Gaps = 7/58 (12%)

Query: 513 LAVFGGAGNVLSLDAIAATRLRIVVRDPSAVDRQRLATLDTAWISADTFHIVVGDAAQ 570
           +A FGG  N+ +LDA   TRLR+ V D + VD+  L  L  A +      +V G   Q
Sbjct: 406 VAAFGGKENITNLDA-CITRLRVSVADVAKVDQAGLKKLGAAGV------VVAGSGVQ 456


Lambda     K      H
   0.325    0.141    0.426 

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: 881
Number of extensions: 52
Number of successful extensions: 8
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: 591
Length of database: 477
Length adjustment: 35
Effective length of query: 556
Effective length of database: 442
Effective search space:   245752
Effective search space used:   245752
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