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 Sep 17 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:

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:

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:

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:

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