GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fruI in Phyllobacterium brassicacearum STM 196

Align Fructose-specific PTS system, I, HPr, and IIA components (characterized)
to candidate WP_106714139.1 CU102_RS26935 phosphoenolpyruvate--protein phosphotransferase

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



>NCBI__GCF_003010955.1:WP_106714139.1
          Length = 661

 Score =  373 bits (958), Expect = e-107
 Identities = 247/661 (37%), Positives = 354/661 (53%), Gaps = 24/661 (3%)

Query: 286 RIALANAH-GLHARPAKILAQLAKSFEGEIRIRIVDGQDSAVSVKSLSKLLSLGARRGQV 344
           R  +   H GLHARPA    +LAKSFE +I +   D    +V+ KS  KL+ LG +    
Sbjct: 3   RSTIVRVHDGLHARPATRFVKLAKSFESDIELVKAD---RSVNAKSSVKLMLLGVKENDE 59

Query: 345 LELIAEPSIAADALPALLRAIEE---GLGEDIEPLPTVSAQSEVIDEITDVVVAPASGCV 401
           + + A  + A +A+ AL+  +E    G+ ED        A+ +V        V P S   
Sbjct: 60  ITVRATGADAIEAVEALIGYLENPNSGILEDGAAEAAKPAEKKVPLGPESSSVGPGSAGK 119

Query: 402 IQAVAAAPGIAIG------PAHIQVLQAIDYPLRGESTAIERERLKTSLADVR-RDIEGL 454
           ++ V A+ G+AIG      PA I+    +   L G+    E  RLK + A V+ R  + L
Sbjct: 120 LRGVPASEGVAIGLAFGFFPAEIKHENRL---LNGDEIPGEVARLKQAFAAVQDRMDKSL 176

Query: 455 IQRSKAKAIREIFITHQEMLDDPELTDEVDTRLKQGESAEAAWMAVIDAAARQQESLQDA 514
              + A++ R I    +++  D ELT  V   +  G  A +A +      A    S+ D 
Sbjct: 177 AATNLAESDRGIIAALKDIAGDDELTGAVAALVDGGIDAVSAVIGATSKIAADFASMDDP 236

Query: 515 LLAERAADLRDIGRRVLAQLCGIETPSEPDQPY--ILVMDEVGPSDVARLDPTRVAGILT 572
            L  RA D+  +GR++   L G +  +    P   IL+ +++G  D+AR    R+AG++ 
Sbjct: 237 YLNARADDVNAVGRQICLALLGQDDANLDAIPAGAILIAEDIGAWDLARAPLKRIAGVIC 296

Query: 573 ARGGATAHSAIVARALGIPALVGAGAAVLRLASGTPLLLDGQRGRLHVDADAATLQRAAE 632
             GGAT+H AI+ARA GIPA++G G +V  L     + LDG  G +  + D AT  R  +
Sbjct: 297 GHGGATSHVAIIARAHGIPAVLGVGRSVQDLQHVNTVALDGNSGDIFPEPDQATADRFHK 356

Query: 633 ERDNREQRLQAAAAQRHQPALTTDGHAVEVFANIGESAGVVSAVEQGAEGIGLLRTELIF 692
           +    E   QA  A R       DG  +E+ AN+G    + +A + GA G+GL RTEL+F
Sbjct: 357 QIGKAESDKQALKAYRDVTPKRADGTVIEIAANLGSLEEIEAAQDAGAMGVGLFRTELLF 416

Query: 693 MAHQQAPDEATQEVEYRRVLDGLAGRPLVVRTLDVGGDKPLPYWPIAKEENPFLGVRGIR 752
           M H   P E  Q   Y  +    A  P++VRTLD+GGDKP+       EENPFLG RGIR
Sbjct: 417 MRHIHLPSEDLQAETYATLAKAFAPYPVIVRTLDIGGDKPISGIDFPAEENPFLGWRGIR 476

Query: 753 LTLQRPQIMEAQLRALLRAADNRPLRIMFPMVGSVDEWRQARDMTERLRLEI-----PVA 807
           + L RP + + QLRALLRAA +  +++M PMV  +DE R AR + E    E+       A
Sbjct: 477 MCLDRPDVFKPQLRALLRAATHGNIKVMLPMVSGLDEVRAARVLIEECADELKREGKAYA 536

Query: 808 DLQLGIMIEVPSAALLAPVLAKEVDFFSVGTNDLTQYTLAIDRGHPTLSAQADGLHPAVL 867
              LG+M+E P+A ++AP+LA+EV FFS+GTNDLTQY +A DR +PT++   D  HPAV+
Sbjct: 537 AFDLGVMVETPAAVMIAPMLAREVAFFSIGTNDLTQYIMAADRLNPTVAKLNDVTHPAVM 596

Query: 868 QLIDITVRAAHAHGKWVGVCGELAADPLAVPVLVGLGVDELSVSARSIGEVKARVRELSL 927
             I++T +A    G  VG+CGE A  P  +P  V +G+ ELS+S  SI   K  V +L  
Sbjct: 597 AAIELTAKAGVEAGIMVGMCGEAAGRPDLIPSFVKMGLTELSMSPSSIPRAKKCVLDLET 656

Query: 928 A 928
           A
Sbjct: 657 A 657


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: 1208
Number of extensions: 56
Number of successful extensions: 3
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: 661
Length adjustment: 41
Effective length of query: 912
Effective length of database: 620
Effective search space:   565440
Effective search space used:   565440
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: 55 (25.8 bits)

This GapMind analysis is from Sep 24 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