GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Pseudomonas simiae WCS417

Align Fructose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate GFF5270 PS417_26985 phosphoenolpyruvate-protein phosphotransferase

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



>FitnessBrowser__WCS417:GFF5270
          Length = 759

 Score =  342 bits (877), Expect = 5e-98
 Identities = 209/562 (37%), Positives = 318/562 (56%), Gaps = 18/562 (3%)

Query: 405 VAAAPGIAIGPAHIQVLQAIDYPLRGESTA----IERERLKTSLADVRRDIEGLIQRSKA 460
           V  +PG A+G A + +L   D  +  + T      E +  KT+L  VR D+  L  +   
Sbjct: 181 VPGSPGAAVGTA-VVMLPPADLDVVPDKTVSDIDAEIKLFKTALEGVRADMRNLSNKLAT 239

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

Query: 518 ERAADLRDIGRRVLAQLCGIETPS--EPDQPYILVMDEVGPSDVARLDPTRVAGILTARG 575
           ERA+D+RD+GRR+LA+L    T +   PD   ILV +E+  + +  +   ++ G+++  G
Sbjct: 300 ERASDVRDLGRRLLAKLQEDRTTNLVYPDNT-ILVSEELTATMLGEVPEGKLVGLVSVLG 358

Query: 576 GATAHSAIVARALGIPALVGAGAAVLRLASGTPLLLDGQRGRLHVDADAATLQRAAEERD 635
              +H AI+ARA+GIP ++G          G  +++DG RG +  +      ++ AE  +
Sbjct: 359 SGNSHVAILARAMGIPTVMGLVDLPYAKVDGIGMIVDGHRGEVFTNPSEVLRKQYAEVVE 418

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

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

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

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

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

Query: 930 VKHLAQLALAVGSANEVRALVE 951
            K L    + + +   + + ++
Sbjct: 718 AKDLLAELMTIDNPQVIHSSLQ 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: 1358
Number of extensions: 67
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