Alignments for a candidate for treEIIA in Cronobacter universalis NCTC 9529

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Cronobacter universalis NCTC 9529

Align PTS system glucose-specific EIICBA component; EC 2.7.1.-; EC 2.7.1.69 (characterized)
to candidate WP_038857764.1 AFK65_RS05470 PTS transporter subunit EIIC

Query= CharProtDB::CH_001857
         (699 letters)



>NCBI__GCF_001277175.1:WP_038857764.1
          Length = 499

 Score =  432 bits (1112), Expect = e-125
 Identities = 235/507 (46%), Positives = 327/507 (64%), Gaps = 46/507 (9%)

Query: 9   LQKIGRALMLPVAILPAAGILLAIGNAMQNKDMIQVLHFLSNDNVQLVAGVMESAGQIVF 68
           L  IGRALMLP+++LPAAG+LLA G+                        +M +AG ++F
Sbjct: 14  LSMIGRALMLPISLLPAAGLLLAFGDKFH-------------------LPLMMNAGGVIF 54

Query: 69  DNLPLLFAVGVAIGLANGDGVAGIAAIIGYLVMNVSMSAVLLANGTIPSDSVERAKFFTE 128
           DNLPLLFA+G A+GLA+  G+A ++A +   ++N+++S  L   G  P  +    K    
Sbjct: 55  DNLPLLFAIGSAVGLASESGIAALSAAVSVFIINITISTQL---GITPEMAASGGK---- 107

Query: 129 NHPAYVNMLGIPTLATGVFGGIIVGVLAALLFNRFYTIELPQYLGFFAGKRFVPIVTSIS 188
               Y  ++GIPTL  GVFGG+I G+LAA  +NRF+T++LP++LGFF+GKRFV I  +  
Sbjct: 108 ----YAMVVGIPTLQMGVFGGLISGILAAWCYNRFHTLQLPEFLGFFSGKRFVAIAAAFL 163

Query: 189 ALILGLIMLVIWPPIQHGLNAFSTGLVEANPTLAAFIFGVIERSLIPFGLHHIFYSPFWY 248
           + +LGL +  +W  IQ G++A S  +   N   + FIFG++ER+LIP GLHHI+Y  FWY
Sbjct: 164 SFLLGLALPYVWQHIQAGIDALSVIVNGDNQAASTFIFGLVERALIPLGLHHIWYPSFWY 223

Query: 249 EFFSYKSAAGEIIRGDQRIFMAQIKDGVQ-------LTAGTFMTGKYPFMMFGLPAAALA 301
            F  Y +  G++I GDQ I+   +++GV+         AG FM G++P M+F LPAA LA
Sbjct: 224 SFGDYTTQTGQVIHGDQTIWFKMLEEGVKSFSSNTYQNAGKFMQGEFPLMLFALPAACLA 283

Query: 302 IYHEAKPQNKKLVAGIMGSAALTSFLTGITEPLEFSFLFVAPVLFAIHCLFAGLSFMVMQ 361
           +YHEA  +NKK+ +GI+ SAALT FLTGITEP+EF+F+FVAPVL+  + + AGL++M M 
Sbjct: 284 MYHEASTKNKKIASGILFSAALTCFLTGITEPVEFTFIFVAPVLYVFNAIMAGLAYMCMY 343

Query: 362 LLNVKIGMTFSGGLIDYFLFGILPN----RTAWWLVIPVGLGLAVIYYFGFRFAIRKFNL 417
           LL+  I  +FS GLIDY  FGILP+    +T +   + VG+ +A+IYYF FRF IR+F++
Sbjct: 344 LLDAHIAKSFSAGLIDYISFGILPSFNGYQTHYLNAVIVGIPMAIIYYFTFRFVIRRFDV 403

Query: 418 KTPGREDAAEETAAPGKTGEAGDLPYEILQAMGDQENIKHLDACITRLRVTVNDQKKVDK 477
           KTPGR D     +A  KT    +L   I+  +G +ENI  + ACITRLR+ V     VDK
Sbjct: 404 KTPGRVDVT--ASADDKTD--AELAGNIVGLLGGKENITSVGACITRLRLEVARPDLVDK 459

Query: 478 DRLKQLGASGVLEVGNN-IQAIFGPRS 503
           D L  LGA GV+ VG+N IQ IFG R+
Sbjct: 460 DGLNGLGARGVVFVGDNGIQVIFGARA 486


Lambda     K      H
   0.323    0.141    0.412 

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: 965
Number of extensions: 48
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: 699
Length of database: 499
Length adjustment: 37
Effective length of query: 662
Effective length of database: 462
Effective search space:   305844
Effective search space used:   305844
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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:

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