Alignments for a candidate for fruI in Pseudomonas fluorescens FW300-N1B4

GapMind for catabolism of small carbon sources

Alignments for a candidate for fruI in Pseudomonas fluorescens FW300-N1B4

Align Fructose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate Pf1N1B4_2284 FIG001592: Phosphocarrier protein kinase/phosphorylase, nitrogen regulation associated

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



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2284
          Length = 759

 Score =  336 bits (861), Expect = 4e-96
 Identities = 205/561 (36%), Positives = 319/561 (56%), Gaps = 16/561 (2%)

Query: 405 VAAAPGIAIGPAHIQVLQA-IDYPLRGESTAIERER--LKTSLADVRRDIEGLIQRSKAK 461
           V  +PG A+G A + +  A +D       T I  E    KT++  VR D+  L  +   +
Sbjct: 181 VPGSPGAAVGTAVVMLPPADLDVVPDKTITDINAELGLFKTAIEGVRADMRALSAKLATQ 240

Query: 462 AI---REIFITHQEMLDDPELTDEVDTRLKQGESAEAAWMAVIDAAARQQESLQDALLAE 518
                R +F  +  MLDD  L  E+ T +K G+ A+ A   V+     + E + DA L E
Sbjct: 241 LRPEERALFDVYLMMLDDASLGSEITTVIKTGQWAQGALRQVVTEHVNRFELMDDAYLRE 300

Query: 519 RAADLRDIGRRVLAQLCGI--ETPSEPDQPYILVMDEVGPSDVARLDPTRVAGILTARGG 576
           RA+D++D+GRR+LA L     +T   PD   ILV +E+ P+ +  +   ++ G+++  G 
Sbjct: 301 RASDVKDLGRRLLAYLQEERQQTLVYPDNT-ILVSEELTPAMLGEVPEGKLVGLVSVLGS 359

Query: 577 ATAHSAIVARALGIPALVGAGAAVLRLASGTPLLLDGQRGRLHVDADAATLQRAAEERDN 636
             +H AI+ARA+GIP ++G          G  +++DG  G ++ +      ++ AE  + 
Sbjct: 360 GNSHVAILARAMGIPTVMGLVDLPYSKVDGIQMIVDGYHGEVYTNPSDVLRKQFAEVVEE 419

Query: 637 REQRLQAAAAQRHQPALTTDGHAVEVFANIGESAGVVSAVEQGAEGIGLLRTELIFMAHQ 696
            +Q      A R  P +T DGH + ++ N G  A V  A ++GAEG+GL RTE+ FM +Q
Sbjct: 420 EKQLALGLDALRDLPCVTVDGHRMPLWVNTGLLADVARAQKRGAEGVGLYRTEVPFMINQ 479

Query: 697 QAPDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIRLTLQ 756
           + P E  Q   YR  L     +P+ +R+LD+GGDK L Y+PI KE+NPFLG RGIR+TL 
Sbjct: 480 RFPSEKEQLAIYREQLAAFHPQPVTMRSLDIGGDKALSYFPI-KEDNPFLGWRGIRVTLD 538

Query: 757 RPQIMEAQLRALLRAADN-RPLRIMFPMVGSVDEWRQARDMTERLRLEI-----PVADLQ 810
            P+I   Q RA+L+A++    LRI+ PM+  + E  +A  +  R   E+      V    
Sbjct: 539 HPEIFLVQTRAMLKASEGLNNLRILLPMISGIHELEEALHLIHRAWGEVRDEGTDVPMPP 598

Query: 811 LGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVLQLI 870
           +G+MIE+P+A      LA++VDF SVG+NDLTQY LA+DR +P ++   D LHPAVLQ +
Sbjct: 599 VGVMIEIPAAVYQTRELARQVDFLSVGSNDLTQYLLAVDRNNPRVADLYDYLHPAVLQAL 658

Query: 871 DITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIGEVKARVRELSLAQV 930
              VR AHA GK V +CGE+A DP A  +L+ +G D LS++A ++ +VK  +R+++L++ 
Sbjct: 659 QNVVRDAHAEGKPVSICGEMAGDPAAAVLLMAMGFDSLSMNATNLPKVKWMLRQINLSKA 718

Query: 931 KHLAQLALAVGSANEVRALVE 951
           K L    + + +   + + ++
Sbjct: 719 KELLAELMTIDNPQVIHSSLQ 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: 1367
Number of extensions: 63
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 Apr 09 2024. 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 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