Alignments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Alignments for a candidate for treEIIA in Pseudomonas fluorescens FW300-N2E3

Align trehalose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate AO353_08465 AO353_08465 phosphoenolpyruvate-protein phosphotransferase

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



>FitnessBrowser__pseudo3_N2E3:AO353_08465
          Length = 759

 Score =  295 bits (755), Expect = 7e-84
 Identities = 192/571 (33%), Positives = 302/571 (52%), Gaps = 29/571 (5%)

Query: 279 GVCASAGSAFGYVVQV---AERTLEMPEFAADQQLERESLERALMHATQALQRLRDNAAG 335
           GV  S G+A G  V +   A+  +   +  AD + E    + A+      ++ L    A 
Sbjct: 180 GVPGSPGAAVGTAVVMLPPADLDVVPDKTIADIEAELGLFKTAIEGVRADMRALSAKLAT 239

Query: 336 EAQAD---IFKAHQELLEDPSLLEQAQALIAEGKSAAFAWNSATEATATLFKSLGSTLLA 392
           + + +   +F  +  +L+D SL  +   +I  G+ A  A           F+ +    L 
Sbjct: 240 QLRPEERALFDVYLMMLDDASLGSEVTTVIKTGQWAQGALRQVVTDHVNRFELMDDAYLR 299

Query: 393 ERALDLMDVGQRVLKLILGVPDGVWELPDQAILIAEQLTPSQTAALDTGKVLGFATVGGG 452
           ERA D+ D+G+R+L  +          PD  ILI+E+LTP+    +  GK++G  +V G 
Sbjct: 300 ERASDVKDLGRRLLAYLQEERQQTLVYPDNTILISEELTPAMLGEVPEGKLVGLVSVLGS 359

Query: 453 ATSHVAILARALGLPAVCGLPLQVLSLASGTRVLLDADKGELHLDPAVSVIEQLHAKRQQ 512
             SHVAILARA+G+P V GL     S   G ++++D   GE++ +P+  + +Q     ++
Sbjct: 360 GNSHVAILARAMGIPTVMGLVDLPYSKVDGIQMIVDGYHGEVYTNPSDVLRKQFADVVEE 419

Query: 513 QRQRHQHELENAARAAVTRDGHHFEVTANVASLAETEQAMSLGAEGIGLLRSEFLYQQRS 572
           ++Q             VT DGH   +  N   LA+  +A   GAEG+GL R+E  +    
Sbjct: 420 EKQLALGLDALRDLPCVTIDGHRMPLWVNTGLLADVARAQKRGAEGVGLYRTEVPFMINQ 479

Query: 573 VAPSHDEQAGTYSAIARALGPQRNLVVRTLDVGGDKPLAYVPMDSEANPFLGMRGIRLCL 632
             PS  EQ   Y     A  PQ  + +R+LD+GGDK L+Y P+  E NPFLG RGIR+ L
Sbjct: 480 RFPSEKEQLAIYREQLAAFHPQP-VTMRSLDIGGDKSLSYFPI-KEDNPFLGWRGIRVTL 537

Query: 633 ERPQLLREQFRAIL-SSAGLARLHIMLPMVSQLSELRLARLMLEEEALALGLRE------ 685
           + P++   Q RA+L +S GL  L I+LPM+S   EL        EEAL L  R       
Sbjct: 538 DHPEIFLVQTRAMLKASEGLNNLRILLPMISGTHEL--------EEALHLIHRAWGEVRD 589

Query: 686 ------LPKLGIMIEVPAAALMADLFAPEVDFFSIGTNDLTQYTLAMDRDHPRLASQADS 739
                 +P +G+MIE+PAA       A +VDF S+G+NDLTQY LA+DR++PR+A   D 
Sbjct: 590 EGTDVPMPPVGVMIEIPAAVYQTKELARQVDFLSVGSNDLTQYLLAVDRNNPRVADLYDY 649

Query: 740 FHPSVLRLIASTVKAAHAHGKWVGVCGALASETLAVPLLLGLGVDELSVSVPLIPAIKAA 799
            HP+VL+ + + V+ AHA GK V +CG +A +  A  LL+ +G D LS++   +P +K  
Sbjct: 650 LHPAVLQALQTVVRDAHAEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLPKVKWM 709

Query: 800 IREVELSDCQAIAHQVLGLESAEQVREALSV 830
           +R++ LS  + +  +++ +++ + +  +L +
Sbjct: 710 LRQINLSWARDLLAELMTIDNPQVIHSSLQL 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: 1266
Number of extensions: 61
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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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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
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