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_038857764.1 AFK65_RS05470 PTS transporter subunit EIIC

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



>NCBI__GCF_001277175.1:WP_038857764.1
          Length = 499

 Score =  347 bits (891), Expect = e-100
 Identities = 202/500 (40%), Positives = 288/500 (57%), Gaps = 60/500 (12%)

Query: 8   KIQRLGRALMLPIAVLPVAGLLLRLGQPDVFNIKMIADAGGAIFDNLPLLFAIGVAVGFA 67
           K+  +GRALMLPI++LP AGLLL  G  D F++ ++ +AGG IFDNLPLLFAIG AVG A
Sbjct: 13  KLSMIGRALMLPISLLPAAGLLLAFG--DKFHLPLMMNAGGVIFDNLPLLFAIGSAVGLA 70

Query: 68  KDNNGVAGLAGAIG-YLIEVAVMKDIN------------------DKLNMGVLSGIVAGI 108
            ++ G+A L+ A+  ++I + +   +                     L MGV  G+++GI
Sbjct: 71  SES-GIAALSAAVSVFIINITISTQLGITPEMAASGGKYAMVVGIPTLQMGVFGGLISGI 129

Query: 109 VAGLLYNRYKDIKLPDYLAFFGGKRFVPIVTGVVCLVLGIAFGYVWQPVQAVIDTAGHWL 168
           +A   YNR+  ++LP++L FF GKRFV I    +  +LG+A  YVWQ +QA ID     +
Sbjct: 130 LAAWCYNRFHTLQLPEFLGFFSGKRFVAIAAAFLSFLLGLALPYVWQHIQAGIDALSVIV 189

Query: 169 TTAG-ALGAFVFGVLNRLLLVTGLHHILNSLTWFVFGTFTPPGGAAVTGDLHRFFA---- 223
                A   F+FG++ R L+  GLHHI     W+ FG +T   G  + GD   +F     
Sbjct: 190 NGDNQAASTFIFGLVERALIPLGLHHIWYPSFWYSFGDYTTQTGQVIHGDQTIWFKMLEE 249

Query: 224 --------GDPTAGTFMTGFFPVMMFGLPAACLAMFHEAPKERRAVVGGLLFSMALTSFL 275
                       AG FM G FP+M+F LPAACLAM+HEA  + + +  G+LFS ALT FL
Sbjct: 250 GVKSFSSNTYQNAGKFMQGEFPLMLFALPAACLAMYHEASTKNKKIASGILFSAALTCFL 309

Query: 276 TGVTEPIEFSFMFLAPVLYVIHALLTGISLAICSALGIHLGFTFSAGAIDYVLNYGL--S 333
           TG+TEP+EF+F+F+APVLYV +A++ G++      L  H+  +FSAG IDY+ ++G+  S
Sbjct: 310 TGITEPVEFTFIFVAPVLYVFNAIMAGLAYMCMYLLDAHIAKSFSAGLIDYI-SFGILPS 368

Query: 334 TRGWW-----AIPIGLVYMVVYYGLFRFFIRKFNMATPGR--EPAAADEQVDSFAAGGFV 386
             G+      A+ +G+   ++YY  FRF IR+F++ TPGR    A+AD++ D+  AG  V
Sbjct: 369 FNGYQTHYLNAVIVGIPMAIIYYFTFRFVIRRFDVKTPGRVDVTASADDKTDAELAGNIV 428

Query: 387 SPVAGTAVPRAQRYIAALGGASNLSVVDACTTRLRLSVVDSNKVSENELKTIGARGVLKR 446
                            LGG  N++ V AC TRLRL V   + V ++ L  +GARGV+  
Sbjct: 429 ---------------GLLGGKENITSVGACITRLRLEVARPDLVDKDGLNGLGARGVVFV 473

Query: 447 GSTNVQVIIGPEADIIADEI 466
           G   +QVI G  A  IA  +
Sbjct: 474 GDNGIQVIFGARAQFIAQSL 493



 Score = 30.0 bits (66), Expect = 2e-04
 Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 4/71 (5%)

Query: 513 LAVFGGAGNVLSLDAIAATRLRIVVRDPSAVDRQRLATL---DTAWISADTFHIVVGDAA 569
           + + GG  N+ S+ A   TRLR+ V  P  VD+  L  L      ++  +   ++ G  A
Sbjct: 428 VGLLGGKENITSVGA-CITRLRLEVARPDLVDKDGLNGLGARGVVFVGDNGIQVIFGARA 486

Query: 570 QRYAEKLATRT 580
           Q  A+ L+  T
Sbjct: 487 QFIAQSLSGMT 497


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: 891
Number of extensions: 44
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: 499
Length adjustment: 35
Effective length of query: 556
Effective length of database: 464
Effective search space:   257984
Effective search space used:   257984
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.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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