GapMind for catabolism of small carbon sources

 

Aligments for a candidate for manP in Escherichia coli BW25113

Align protein-Npi-phosphohistidine-D-mannose phosphotransferase (EC 2.7.1.191) (characterized)
to candidate 14863 b0731 fused 2-O-a-mannosyl-D-glycerate specific PTS enzymes: IIA component/IIB component/IIC component (NCBI)

Query= BRENDA::O31645
         (650 letters)



>lcl|FitnessBrowser__Keio:14863 b0731 fused
           2-O-a-mannosyl-D-glycerate specific PTS enzymes: IIA
           component/IIB component/IIC component (NCBI)
          Length = 658

 Score =  278 bits (710), Expect = 7e-79
 Identities = 176/463 (38%), Positives = 258/463 (55%), Gaps = 29/463 (6%)

Query: 3   LLAITSCPNGIAHTYMAAENLQKAADRLGVSIKVETQGGIGVENKLTEEEIREADAIIIA 62
           ++ +T+CP GIAHTYMAAE L+KA  +LGV++ VE QG  G+E +LT +++  A A I A
Sbjct: 186 IVCVTACPAGIAHTYMAAEYLEKAGRKLGVNVYVEKQGANGIEGRLTADQLNSATACIFA 245

Query: 63  ADRSVNK-DRFIGKKLLSVGVQDGIRKPEELIQKALNGDIPVYRS-ATKSESGNHQEKK- 119
           A+ ++ + +RF G   LSV V + IR  E LIQ+AL     + RS  T++   + Q  K 
Sbjct: 246 AEVAIKESERFNGIPALSVPVAEPIRHAEALIQQALT----LKRSDETRTVQQDTQPVKS 301

Query: 120 -QNPIYRHLMNGVSFMVPFIVVGGLLIAVALTLGGEKTPKGLVIPDDSFWKTIEQIGSAS 178
            +  + + L++G+SF VP IV GG ++AVA+ L      + L   ++S+     ++G   
Sbjct: 302 VKTELKQALLSGISFAVPLIVAGGTVLAVAVLLSQIFGLQDLFNEENSWLWMYRKLGGGL 361

Query: 179 FSF-MIPILAGYIAYSIADKPGLVPGMIGGYIAATGSFYDSASGAGFLGGIIAGFLAGYA 237
               M+P+LA Y AYS+ADKP L PG   G  A       +  G+GFLG ++ G +AGY 
Sbjct: 362 LGILMVPVLAAYTAYSLADKPALAPGFAAGLAA-------NMIGSGFLGAVVGGLIAGYL 414

Query: 238 ALWIKK-LKVPKAIQPIMPIIIIPVFASLIVGLAFVFLIGAPVAQIFASLTVWLAGMKGS 296
             W+K  L++       +   + PV  +L  G   +F++G PVA I  SLT WL G+ GS
Sbjct: 415 MRWVKNHLRLSSKFNGFLTFYLYPVLGTLGAGSLMLFVVGEPVAWINNSLTAWLNGLSGS 474

Query: 297 SSILLALILGAMISFDMGGPVNKVAFLFGSAMIGEGNYEIMGPIAVAICIPPIG---LGI 353
           +++LL  ILG M SFD+GGPVNK A+ F    +  G Y   GP A+   +  +    +  
Sbjct: 475 NALLLGAILGFMCSFDLGGPVNKAAYAFCLGAMANGVY---GPYAIFASVKMVSAFTVTA 531

Query: 354 ATFLGKRKFEASQREMGKAAFTMGLFGITEGAIPFAAQDPLRVIPSIMAGSMTGSVIAMI 413
           +T L  R F+  + E GK+ + +GL GITEGAIP A +DPLRVI S + GSM    I   
Sbjct: 532 STMLAPRLFKEFEIETGKSTWLLGLAGITEGAIPMAIEDPLRVIGSFVLGSMVTGAIVGA 591

Query: 414 GNVGDRVAHGGPIVAVL------GAVDHVLMFFIAVIAGSLVT 450
            N+G      G     L      G V   + +F A + G+ ++
Sbjct: 592 MNIGLSTPGAGIFSLFLLHDNGAGGVMAAIGWFGAALVGAAIS 634



 Score = 88.2 bits (217), Expect = 1e-21
 Identities = 46/148 (31%), Positives = 78/148 (52%), Gaps = 1/148 (0%)

Query: 502 LTDIISPELIEPNLSGETSDDIIDELIQKLSRRGALLSESGFKQAILNREQQGTTAIGMN 561
           LT +   + +  N    + ++ I  L Q+L+  G + S   F + +  RE  G TA+G  
Sbjct: 23  LTTLTHRDALCLNARFTSREEAIHALTQRLAALGKISSTEQFLEEVYRRESLGPTALGEG 82

Query: 562 IAIPHGKSEAVREPSVAFGIKRSGVDWNSLDGSEA-KLIFMIAVPKESGGNQHLKILQML 620
           +A+PHGK+ AV+E + A       + W  +DG EA  L+ ++A+P    G  H+++L  L
Sbjct: 83  LAVPHGKTAAVKEAAFAVATLSEPLQWEGVDGPEAVDLVVLLAIPPNEAGTTHMQLLTAL 142

Query: 621 SRKLMDDNYRERLLSVQTTEEAYKLLEE 648
           + +L DD  R R+ S  T +E    L++
Sbjct: 143 TTRLADDEIRARIQSATTPDELLSALDD 170


Lambda     K      H
   0.319    0.137    0.386 

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: 925
Number of extensions: 50
Number of successful extensions: 7
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 650
Length of database: 658
Length adjustment: 38
Effective length of query: 612
Effective length of database: 620
Effective search space:   379440
Effective search space used:   379440
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: 54 (25.4 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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