Aligments for a candidate for fruI in Pseudomonas fluorescens FW300-N2E3

GapMind for catabolism of small carbon sources

Aligments for a candidate for fruI in Pseudomonas fluorescens FW300-N2E3

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

Query= reanno::pseudo3_N2E3:AO353_05485
         (953 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_08465
          Length = 759

 Score =  333 bits (853), Expect = 3e-95
 Identities = 202/562 (35%), Positives = 318/562 (56%), Gaps = 18/562 (3%)

Query: 405 VAAAPGIAIGPAHIQVLQAIDYPLRGESTAIERER----LKTSLADVRRDIEGLIQRSKA 460
           V  +PG A+G A + +L   D  +  + T  + E      KT++  VR D+  L  +   
Sbjct: 181 VPGSPGAAVGTA-VVMLPPADLDVVPDKTIADIEAELGLFKTAIEGVRADMRALSAKLAT 239

Query: 461 KAI---REIFITHQEMLDDPELTDEVDTRLKQGESAEAAWMAVIDAAARQQESLQDALLA 517
           +     R +F  +  MLDD  L  EV T +K G+ A+ A   V+     + E + DA L 
Sbjct: 240 QLRPEERALFDVYLMMLDDASLGSEVTTVIKTGQWAQGALRQVVTDHVNRFELMDDAYLR 299

Query: 518 ERAADLRDIGRRVLAQLCGI--ETPSEPDQPYILVMDEVGPSDVARLDPTRVAGILTARG 575
           ERA+D++D+GRR+LA L     +T   PD   IL+ +E+ P+ +  +   ++ G+++  G
Sbjct: 300 ERASDVKDLGRRLLAYLQEERQQTLVYPDNT-ILISEELTPAMLGEVPEGKLVGLVSVLG 358

Query: 576 GATAHSAIVARALGIPALVGAGAAVLRLASGTPLLLDGQRGRLHVDADAATLQRAAEERD 635
              +H AI+ARA+GIP ++G          G  +++DG  G ++ +      ++ A+  +
Sbjct: 359 SGNSHVAILARAMGIPTVMGLVDLPYSKVDGIQMIVDGYHGEVYTNPSDVLRKQFADVVE 418

Query: 636 NREQRLQAAAAQRHQPALTTDGHAVEVFANIGESAGVVSAVEQGAEGIGLLRTELIFMAH 695
             +Q      A R  P +T DGH + ++ N G  A V  A ++GAEG+GL RTE+ FM +
Sbjct: 419 EEKQLALGLDALRDLPCVTIDGHRMPLWVNTGLLADVARAQKRGAEGVGLYRTEVPFMIN 478

Query: 696 QQAPDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTL 755
           Q+ P E  Q   YR  L     +P+ +R+LD+GGDK L Y+PI KE+NPFLG RGIR+TL
Sbjct: 479 QRFPSEKEQLAIYREQLAAFHPQPVTMRSLDIGGDKSLSYFPI-KEDNPFLGWRGIRVTL 537

Query: 756 QRPQIMEAQLRALLRAADN-RPLRIMFPMVGSVDEWRQARDMTERLRLEI-----PVADL 809
             P+I   Q RA+L+A++    LRI+ PM+    E  +A  +  R   E+      V   
Sbjct: 538 DHPEIFLVQTRAMLKASEGLNNLRILLPMISGTHELEEALHLIHRAWGEVRDEGTDVPMP 597

Query: 810 QLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQL 869
            +G+MIE+P+A      LA++VDF SVG+NDLTQY LA+DR +P ++   D LHPAVLQ 
Sbjct: 598 PVGVMIEIPAAVYQTKELARQVDFLSVGSNDLTQYLLAVDRNNPRVADLYDYLHPAVLQA 657

Query: 870 IDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIGEVKARVRELSLAQ 929
           +   VR AHA GK V +CGE+A DP A  +L+ +G D LS++A ++ +VK  +R+++L+ 
Sbjct: 658 LQTVVRDAHAEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLPKVKWMLRQINLSW 717

Query: 930 VKHLAQLALAVGSANEVRALVE 951
            + L    + + +   + + ++
Sbjct: 718 ARDLLAELMTIDNPQVIHSSLQ 739


Lambda     K      H
   0.319    0.135    0.383 

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: 1389
Number of extensions: 64
Number of successful extensions: 4
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: 953
Length of database: 759
Length adjustment: 42
Effective length of query: 911
Effective length of database: 717
Effective search space:   653187
Effective search space used:   653187
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 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, 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