GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Pseudomonas simiae WCS417

Align Phosphoenolpyruvate--protein phosphotransferase (EC 2.7.3.9) (characterized)
to candidate GFF780 PS417_03965 PTS fructose transporter subunit IIA

Query= reanno::WCS417:GFF780
         (952 letters)



>FitnessBrowser__WCS417:GFF780
          Length = 952

 Score = 1830 bits (4740), Expect = 0.0
 Identities = 952/952 (100%), Positives = 952/952 (100%)

Query: 1   MLELTVEQISMGQVAVDKSAALHLLAEKLVADGLVAEGYLSGLQAREAQGSTFLGQGIAI 60
           MLELTVEQISMGQVAVDKSAALHLLAEKLVADGLVAEGYLSGLQAREAQGSTFLGQGIAI
Sbjct: 1   MLELTVEQISMGQVAVDKSAALHLLAEKLVADGLVAEGYLSGLQAREAQGSTFLGQGIAI 60

Query: 61  PHGTPETRDQVFSTGVRLLQFPEGVDWGDGQIVYLAIGIAAKSDEHLRLLQLLTRALGET 120
           PHGTPETRDQVFSTGVRLLQFPEGVDWGDGQIVYLAIGIAAKSDEHLRLLQLLTRALGET
Sbjct: 61  PHGTPETRDQVFSTGVRLLQFPEGVDWGDGQIVYLAIGIAAKSDEHLRLLQLLTRALGET 120

Query: 121 DLGQALRRAGSAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS 180
           DLGQALRRAGSAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS
Sbjct: 121 DLGQALRRAGSAEALLKLLQGAPQELALDAQMIGLGVSADDFEELVWRGARLLRQADCVS 180

Query: 181 NGFAAVLQQVDALPLGDGLWWLHSEQTVKRPGLAFVTPDKPMRYLGQPLNGLFCLASLGE 240
           NGFAAVLQQVDALPLGDGLWWLHSEQTVKRPGLAFVTPDKPMRYLGQPLNGLFCLASLGE
Sbjct: 181 NGFAAVLQQVDALPLGDGLWWLHSEQTVKRPGLAFVTPDKPMRYLGQPLNGLFCLASLGE 240

Query: 241 AHQTLLERLCALLIEGRGQELGRATSSRAVLEVLGGELPPDWPAARITLANAHGLHARPA 300
           AHQTLLERLCALLIEGRGQELGRATSSRAVLEVLGGELPPDWPAARITLANAHGLHARPA
Sbjct: 241 AHQTLLERLCALLIEGRGQELGRATSSRAVLEVLGGELPPDWPAARITLANAHGLHARPA 300

Query: 301 KILAQLAKSFDGDLRVRIVDGPVGAVSVKSLSKLLSLGARRGQVLEFIAEPSIAGDALPA 360
           KILAQLAKSFDGDLRVRIVDGPVGAVSVKSLSKLLSLGARRGQVLEFIAEPSIAGDALPA
Sbjct: 301 KILAQLAKSFDGDLRVRIVDGPVGAVSVKSLSKLLSLGARRGQVLEFIAEPSIAGDALPA 360

Query: 361 LLAAVEEGLGEDVEPLPTLSVQPEVLDIEPELSAPLAGSQVQAIAAAPGIAIGPAHIQVL 420
           LLAAVEEGLGEDVEPLPTLSVQPEVLDIEPELSAPLAGSQVQAIAAAPGIAIGPAHIQVL
Sbjct: 361 LLAAVEEGLGEDVEPLPTLSVQPEVLDIEPELSAPLAGSQVQAIAAAPGIAIGPAHIQVL 420

Query: 421 QVFDYPLRGESCAIERERLHSALADVRRDIQGLIERSQSKAIREIFVTHQEMLDDPELTD 480
           QVFDYPLRGESCAIERERLHSALADVRRDIQGLIERSQSKAIREIFVTHQEMLDDPELTD
Sbjct: 421 QVFDYPLRGESCAIERERLHSALADVRRDIQGLIERSQSKAIREIFVTHQEMLDDPELTD 480

Query: 481 EVDTRLKQGESAEAAWMSVIEAAAKQQESLQDALLAERAADLRDIGRRVLAQLCGVETSQ 540
           EVDTRLKQGESAEAAWMSVIEAAAKQQESLQDALLAERAADLRDIGRRVLAQLCGVETSQ
Sbjct: 481 EVDTRLKQGESAEAAWMSVIEAAAKQQESLQDALLAERAADLRDIGRRVLAQLCGVETSQ 540

Query: 541 EPSEPYILVMDEVGPSDVARLDPARVAGILTARGGATAHSAIVARALGIPALVGAGPAVL 600
           EPSEPYILVMDEVGPSDVARLDPARVAGILTARGGATAHSAIVARALGIPALVGAGPAVL
Sbjct: 541 EPSEPYILVMDEVGPSDVARLDPARVAGILTARGGATAHSAIVARALGIPALVGAGPAVL 600

Query: 601 LLAAGTPLLLDGQRGRLHVDADAATLQRATVERDTREQRLQAASAQRHEPALTRDGHAVE 660
           LLAAGTPLLLDGQRGRLHVDADAATLQRATVERDTREQRLQAASAQRHEPALTRDGHAVE
Sbjct: 601 LLAAGTPLLLDGQRGRLHVDADAATLQRATVERDTREQRLQAASAQRHEPALTRDGHAVE 660

Query: 661 VFANIGESAGVASAVEQGAEGIGLLRTELIFMAHPQAPDEATQEAEYRRVLDGLAGRPLV 720
           VFANIGESAGVASAVEQGAEGIGLLRTELIFMAHPQAPDEATQEAEYRRVLDGLAGRPLV
Sbjct: 661 VFANIGESAGVASAVEQGAEGIGLLRTELIFMAHPQAPDEATQEAEYRRVLDGLAGRPLV 720

Query: 721 VRTLDVGGDKPLPYWPIAEEENPFLGVRGIRLTLQRPQIMEAQLRALLRSADNRPLRIMF 780
           VRTLDVGGDKPLPYWPIAEEENPFLGVRGIRLTLQRPQIMEAQLRALLRSADNRPLRIMF
Sbjct: 721 VRTLDVGGDKPLPYWPIAEEENPFLGVRGIRLTLQRPQIMEAQLRALLRSADNRPLRIMF 780

Query: 781 PMVGSVDEWRAARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDL 840
           PMVGSVDEWRAARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDL
Sbjct: 781 PMVGSVDEWRAARDMTERLRLEIPVADLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDL 840

Query: 841 TQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLV 900
           TQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLV
Sbjct: 841 TQYTLAIDRGHPTLSAQADGLHPAVLQLIDITVRAAHAHGKWVGVCGELAADPLAVPVLV 900

Query: 901 GLGVDELSVSARSIPEVKARVREFSLSEAQGLAQKALAVGSPAEVRALVEAV 952
           GLGVDELSVSARSIPEVKARVREFSLSEAQGLAQKALAVGSPAEVRALVEAV
Sbjct: 901 GLGVDELSVSARSIPEVKARVREFSLSEAQGLAQKALAVGSPAEVRALVEAV 952


Lambda     K      H
   0.318    0.135    0.385 

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: 2649
Number of extensions: 87
Number of successful extensions: 1
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: 952
Length of database: 952
Length adjustment: 44
Effective length of query: 908
Effective length of database: 908
Effective search space:   824464
Effective search space used:   824464
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: 57 (26.6 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