Aligments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Aligments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2C3

Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate AO356_10350 AO356_10350 phosphoenolpyruvate-protein phosphotransferase

Query= reanno::pseudo3_N2E3:AO353_15995
         (844 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_10350
          Length = 759

 Score =  298 bits (764), Expect = 6e-85
 Identities = 205/619 (33%), Positives = 319/619 (51%), Gaps = 39/619 (6%)

Query: 236 EDAELAISTLAQLLADGCGEAVTPVAVVAPVVEAQEVSTKLLRGVCASAGSAFGYVVQ-- 293
           E  E  + T++  LA     A    ++     + + +      GV  S G+A G  V   
Sbjct: 137 EGEEAFLVTMSAQLAGVIAHAEATGSISGLGRQGKGIQEAKFVGVPGSPGAAVGTAVVML 196

Query: 294 -------VAERTLEMPEFAADQQLERESLE--RALMHATQALQRLRDNAAGEAQADIFKA 344
                  V ++T+   +  A+  L + ++E  RA M A  A  +L      E +A +F  
Sbjct: 197 PPADLDVVPDKTIT--DINAELGLFKTAIEGVRADMRALSA--KLATQLRPEERA-LFDV 251

Query: 345 HQELLEDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLAERALDLMDVGQR 404
           +  +L+D SL  +   +I  G+ A  A           F+ +    L ERA D+ D+G+R
Sbjct: 252 YLMMLDDASLGSEVTTVIKTGQWAQGALRQVVTDHVNRFELMDDAYLRERASDVKDLGRR 311

Query: 405 VLKLILGVPDGVWELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGGATSHVAILARAL 464
           +L  +          PD  IL++E+LTP+    +  GK+ G  +V G   SHVAILARA+
Sbjct: 312 LLAYLQQERQQTLVYPDNTILVSEELTPAMLGEVPEGKLAGLVSVLGSGNSHVAILARAM 371

Query: 465 GLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQQRQRHQHELENA 524
           G+P V GL     S   G ++++D   GE++ +P+  + +Q     ++++Q         
Sbjct: 372 GIPTVMGLVDLPYSKVDGIQMIVDGYHGEVYTNPSDVLRKQFADVVEEEKQLSLGLDALR 431

Query: 525 ARAAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRSVAPSHDEQAGTY 584
               VT DGH   +  N   LA+  +A   GAEG+GL R+E  +      PS  EQ   Y
Sbjct: 432 DLPCVTLDGHRMPLWVNTGLLADVARAQKRGAEGVGLYRTEVPFMINQRFPSEKEQLAIY 491

Query: 585 SAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCLERPQLLREQFRA 644
                A  PQ  + +R+LD+GGDK L+Y P+  E NPFLG RGIR+ L+ P++   Q RA
Sbjct: 492 REQLAAFHPQP-VTMRSLDIGGDKSLSYFPI-KEDNPFLGWRGIRVTLDHPEIFLVQARA 549

Query: 645 IL-SSAGLARLHIMLPMVSQLSELRLARLMLEEEALALGLRE------------LPKLGI 691
           +L +S GL  L I+LPM+S   EL        EEAL L  R             +P +G+
Sbjct: 550 MLKASEGLNNLRILLPMISGTHEL--------EEALHLIHRAWGEVRDEGTDVPMPPVGV 601

Query: 692 MIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADSFHPSVLRLIAST 751
           MIE+PAA       A +VDF S+G+NDLTQY LA+DR++PR+A   D  HP+VL+ + + 
Sbjct: 602 MIEIPAAVYQTKELARQVDFLSVGSNDLTQYLLAVDRNNPRVADLYDYLHPAVLQALQNV 661

Query: 752 VKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAAIREVELSDCQAI 811
           V+ AHA GK V +CG +A +  A  LL+ +G D LS++   +P +K  +R++ LS  Q +
Sbjct: 662 VRDAHAEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLPKVKWMLRQINLSKAQEL 721

Query: 812 AHQVLGLESAEQVREALSV 830
             +V+ +++ + +  +L +
Sbjct: 722 LAEVMTIDNPQVIHSSLQL 740


Lambda     K      H
   0.318    0.132    0.370 

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: 1255
Number of extensions: 56
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: 1
Length of query: 844
Length of database: 759
Length adjustment: 41
Effective length of query: 803
Effective length of database: 718
Effective search space:   576554
Effective search space used:   576554
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Protein sequences (fasta format)
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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 paper from 2022 on GapMind for carbon sources, or view the source code.

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